Cheminfomatics & Molecular Modeling Sites

3D Structure Conformer Generation

Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
BALL BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed for this purpose.
BioPharmics Fast, accurate and robust 3D modelling from small molecules to large macrocycles
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
ChemPen3D ChemPen3D is developed by ChemPen Software and is used by 1 user of Software Informer. The most popular version of this product among our users is 1.7
ConfGen Combines empirical heuristics with physics-based calculations to efficiently produce diverse, low-energy 3D conformers of small molecules for virtual screening
CONFLEX CONFLEX permits fast, accurate, automated conformation searching and analysis critical to drug discovery and chemical engineering.
Corina Classic CORINA is a fast and powerful 3D structure generator for small and medium-sized, drug-like molecules.
COSMOS Computer Simulation of Molecular Structures
CSD Conformer Generator Generates high-quality 3D conformers based on experimental data from the Cambridge Structural Database, aiding in drug discovery and materials science applications. (Free for academic use)
DataWarrior An Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. (open source)
FANTOM The main purpose of the program FANTOM (Fast Newton-Raphson Torsion Angle Minimizer) is to calculate low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments.
Frog2 This repository contains the full source code of Frog2, a tool devoted to the 2D/3D generation of ensemble of conformations for small drug-like compounds.
Gypsum-DL Gypsum-DL is a free, open-source program for preparing 3D small-molecule models. Beyond simply assigning atomic coordinates, Gypsum-DL accounts for alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
Indigo Toolkit Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization.
Lig3DLens An end-to-end computational toolbox for 3D virtual screening based on shape and electrostatics similarity, utilizing RDKit for conformer generation and alignment. (open source)
LigPrep LigPrep is a tool to robustly and rapidly prepare high-quality small molecule ligand structures for structure-based virtual screening and other computational workflows.
MacroModel Versatile, full-featured molecular modeling program
Millsian Millsian, Inc., is the future of molecular modeling. Utilizing a new classical approach to solving atoms and molecules, our software will help researchers design the next generation of pharmaceuticals.
Molassembler A graph-based molecule construction tool supporting both organic and inorganic molecules, offering stereoisomer control and conformer generation through distance geometry methods
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Molinspiration Galaxy 3D Structure Generator Galaxy 3D Structure Generator
Moloc a Molecular Design Software Suite
MolView MolView is an application for sketching and viewing small molecular structures. You can export images and find references to chemical information.
OMEGA OMEGA is designed to sample accurately the conformational space of a wide variety of molecules.
Online SMILES Translator and Structure File Generator Online SMILES Translator and Structure File Generator
Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
pDynamo pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC),
RACHEL RACHEL is an all-purpose ligand refinement software package designed to combinatorially derivatize a lead compound to improve ligand-receptor binding and accelerate drug discovery.
RDKit RDKit: Open-Source Cheminformatics Software
shape Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.
Small molecule conformer generation Simple webapp to generate small ligand conformers for docking using RDKit.
VConf VConf is a powerful and flexible conformational search application which processes an SD file of drug-like compounds containing an initial 2D or 3D conformation of each molecule.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.

ADME/PK prediction

ACDLABs Absolv Absolv calculate Abraham Solvation Parameters and various solvation-related properties of solutes, directly from structure.
ACDLABs ADME Suite ACD/ADME Suite is a collection of prediction modules that provide high-quality, structure-based calculations of pharmacokinetic properties.
ACDLabs The Percepta Platform The Percepta Platform is a portfolio of software applications and a technology ecosystem for predicting and managing physicochemical, ADME/Tox, and other molecular property data.
ADMET Predictor ADMET Predictor® leads with unique capabilities for discovery PK assessment and deployment to medicinal chemistry and DMPK teams!
ADMETlab 3.0 Undesirable pharmacokinetics and toxicity are major contributors to drug development failures. It is widely recognized that evaluating the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of chemicals early on is crucial.
admetSAR A comprehensive source and free tool for evaluating chemical ADMET properties admetSAR is free for non-commercial use only.
AMBIT AMBIT is an open chemoinformatic system designed to support companies by facilitating chemical safety assessment.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA QSAR, ADMET & Predictive Toxicology (TOPKAT) Tools for Designing Therapeutics with Favorable Pharmacokinetic Properties and Safety Profiles
Cefic-LR Cefic-LRI updates online toolbox for chemical risk assessment Cefic’s Long Range Research Initiative (LRI) has updated some of its quality-assured databases and key prediction tools for risk assessment and toxicity testing of chemicals.
CERTARA Phoenix Trusted PK/PD analysis for preclinical and clinical insights
Danish (Q)SAR Database The Danish QSAR database has been freely available on the internet since 2004. It is a tool that allows industry, research, authorities and others to search for hazard information on chemical substances, especially those with little or no testing data
Deep-PK Deep-PK : deep learning for small molecule pharmacokinetic and toxicity prediction
EPI Suite The EPI (Estimation Programs Interface) Suite™ is a Windows®-based suite of physical/chemical property and environmental fate estimation programs developed by EPA’s and Syracuse Research Corp. (SRC).
Frog2 This repository contains the full source code of Frog2, a tool devoted to the 2D/3D generation of ensemble of conformations for small drug-like compounds.
GastroPlus Modeling and simulation package – supporting internal research through regulatory filings.
Lilly-Medchem-Rules his is an implementation of Eli Lilly Medchem Rules. They were published under “Rules for Identifying Potentially Reactive or Promiscuous Compounds” by Robert F. Bruns and Ian W. Watson, J. Med. Chem. 2012, 55, 9763-9772.
MedChem Designer Our FREE chemical sketching software tool which combines innovative molecule drawing features with a few fast and accurate ADMET property predictions from our top-ranked ADMET Predictor software, including logP, logD(7.4), Polar Surface Area, and Lipinski
META Ultra Calculate the probability of metabolite formation and screen for toxicity potential
MetaPred MetaPred Server predict metabolizing CYP isoform of a drug molecule/substrate, based on SVM models developed using CDK descriptors.
MetaSite MetaSite is a computational procedure that predicts metabolic transformations related to cytochrome and flavin-containing monooxygenase mediated reactions in phase I metabolism.
OSIRIS Property Explorer The OSIRIS Property Explorer lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid.
PaDEL-DDPredictor A software to calculate pharmacodynamics, pharmacokinetics and toxicological properties of compounds.
Pallas System ADME prediction software family to boost your R&D productivity
PASS Chemo-Informatics. Compute biological activity for a compound library
PK-Sim PK-Sim® and MoBi® for PBPK and Quantitative Systems Pharmacology
PreADMET PreADMET is a web-based application for predicting ADME/Tox data and building drug-like chemical library using in silico screening method
QikProp QikProp is an advanced tool for predicting pharmacokinetic and physicochemical (ADME) properties of small organic molecules based on the full 3D molecular structure.
QSAR TOOLBOX The Toolbox is a free software application that supports reproducible and transparent chemical hazard assessment.
rd_filters This script provides a simple means of applying the functional group filters from the ChEMBL database, as well as a number of property filters from the RDKit, to a set of compounds.
Semeta Predict Phase I and II metabolic routes, sites, products and lability
Simcyp™ PBPK Simulator The Simcyp PBPK Simulator is the industry leader and most widely adopted platform for PBPK modeling in drug development.
SKIN-CAD SKIN-CAD is software for skin-body pharmacokinetic simulation developed based on percutaneous absorption model
StarDrop StarDrop™ enables a seamless flow from the latest data through predictive modelling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process.
SwissADME This website allows you to compute physicochemical descriptors as well as to predict ADME parameters, pharmacokinetic properties, druglike nature and medicinal chemistry friendliness of one or multiple small molecules to support drug discovery.
TIMES TIMES (tissue metabolism simulator) is a heuristic algorithm used to generate plausible metabolic maps from a comprehensive library of biotransformations and abiotic reactions.
VEGA QSAR Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes.
VolSurf+ VolSurf+ creates 128 molecular descriptors from 3D Molecular Interaction Fields (MIFs) produced by our software GRID, which are particularly relevant to ADME prediction and are also simple to interpret.

Toxicity prediction

ACDLABs Tox Suite Tox Suite is a collection of prediction modules that offer insightful, structure-based calculations of toxicity.
ADMET Predictor ADMET Predictor® leads with unique capabilities for discovery PK assessment and deployment to medicinal chemistry and DMPK teams!
ADMETlab 3.0 Undesirable pharmacokinetics and toxicity are major contributors to drug development failures. It is widely recognized that evaluating the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of chemicals early on is crucial.
admetSAR A comprehensive source and free tool for evaluating chemical ADMET properties admetSAR is free for non-commercial use only.
AMBIT AMBIT is an open chemoinformatic system designed to support companies by facilitating chemical safety assessment.
Bioalerts Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets. (open source)
BIOVIA QSAR, ADMET & Predictive Toxicology (TOPKAT) Tools for Designing Therapeutics with Favorable Pharmacokinetic Properties and Safety Profiles
CASE Ultra CASE Ultra is software program used in computational toxicology that identifies structural alerts related to toxicity using (Q)SAR.
CATALOGIC The CATALOGIC software suite is a platform for models and databases related to the environment fate of chemicals such as abiotic and biotic degradation, bioaccumulation and acute aquatic toxicity.
Cefic-LR Cefic-LRI updates online toolbox for chemical risk assessment Cefic’s Long Range Research Initiative (LRI) has updated some of its quality-assured databases and key prediction tools for risk assessment and toxicity testing of chemicals.
ChemProp There is a public free edition based on developments within the former EU Integrated Project OSIRIS. Furthermore, there is a professional version covering all features including batch processing in terms of QSAR runs for compound lists.
ChemTunes·ToxGPS ChemTunes·ToxGPS® is a unique cheminformatics platform and expert QC’ed database to store, manage, search, and retrieve chemical substances along with their in vitro and in vivo toxicity, safety evaluation and metabolism data.
CRANIUM – Property Estimation Software Cranium is physical property estimation software package.
Danish (Q)SAR Database The Danish QSAR database has been freely available on the internet since 2004. It is a tool that allows industry, research, authorities and others to search for hazard information on chemical substances, especially those with little or no testing data
Deep-PK Deep-PK : deep learning for small molecule pharmacokinetic and toxicity prediction
Derek Nexus Derek Nexus is an expert-knowledge based software, which can help you to meet ICH M7 by providing fast and accurate toxicity predictions.
DMax Intelligent stand for exploring schemes of cross biological, chemical and clinical domains.
EPI Suite The EPI (Estimation Programs Interface) Suite™ is a Windows®-based suite of physical/chemical property and environmental fate estimation programs developed by EPA’s and Syracuse Research Corp. (SRC).
eTOXlab eTOXlab has been developed for the eTOX project. The eTOX project was a collaborative initiative launched in 2010 as a temporary consortium aimed at improving the prediction of drug toxicities.
HazardExpert Pro HazardExpert is an ideal tool for quick prediction of compound’s toxicity in the drug discovery process or during the dispositional research phase.
Janus Janus is a specific application to prioritize and screen substances, considering PBT (persistent, bioaccumulative and toxic), CMR (carcinogenic, mutagenic and reprotoxic), as well as chemicals supposed to be endocrine disruptors.
Leadscope Leadscope Model Applier is a powerful, easy-to-use software solution for computational toxicology, providing accurate toxicity predictions, expert review capabilities, and regulatory-ready reports in seconds.
OncoLogic The OncoLogic™ model is an expert system that mimics the judgment of human experts by following sets of knowledge rules based on studies of how chemicals cause cancer in animals and humans.
OSIRIS Property Explorer The OSIRIS Property Explorer lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid.
PaDEL-DDPredictor A software to calculate pharmacodynamics, pharmacokinetics and toxicological properties of compounds.
Pallas System ADME prediction software family to boost your R&D productivity
PASS Chemo-Informatics. Compute biological activity for a compound library
PreADMET PreADMET is a web-based application for predicting ADME/Tox data and building drug-like chemical library using in silico screening method
pred-herg Unlocking the Full Potential of Predictive Modeling for Precise hERG Activity Predictions
PRED-SKIN The Pred-Skin application is based on externally predictive QSAR models of skin sensitization.
QSAR TOOLBOX The Toolbox is a free software application that supports reproducible and transparent chemical hazard assessment.
RAIS (Risk Assessment Information System) RAIS (Risk Assessment Information System)
Sarah Nexus Sarah Nexus is a statistical-based software which can help you to meet ICH M7 by identifying potentially toxic chemicals through the prediction of mutagenicity.
SpheraCosmolife SpheraCosmolife is a unique application for cosmetic ingredients risk assessment, covering both exposure and hazard.
StarDrop StarDrop™ enables a seamless flow from the latest data through predictive modelling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process.
TerraQSAR All TerraQSAR programs use proprietary neural networks for the computation of biological effects and physico-chemical properties of defined chemicals.
TIMES TIMES (tissue metabolism simulator) is a heuristic algorithm used to generate plausible metabolic maps from a comprehensive library of biotransformations and abiotic reactions.
ToxiPred Toxipred is a server where user can submit chemical molecules in the commonly used format (mol/SMILE/sdf) and after descriptors calculation our server would predict the pIGC50 value of the molecule.
Toxmatch Chemical Landscape Analysis with OpenTox
Toxtree https://toxtree.sourceforge.net/#:~:text=Toxtree%20is%20a%20full%2Dfeatured%20and%20flexible%20user%2Dfriendly%20open%20source%20application%2C%20which%20is%20able%20to%20estimate%20toxic%20hazard%20by%20applying%20a%20decision%20tree%20approach.
VEGA QSAR Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes.
ViTAL ViTAL is a comprehensive toxicity prediction platform which provides multiple levels of toxicity alerts in compliance with the requirements of regulatory authorities for product approval.

Properties Prediction

ACDLABs Absolv Absolv calculate Abraham Solvation Parameters and various solvation-related properties of solutes, directly from structure.
ACDLABs PhysChem Suite ACD/PhysChem Suite is made up of a number of prediction modules. It provides high-quality, structure-based calculations of physicochemical properties.
alvaModel AlvaModel is a software tool to create Quantitative Structure Activity/Property Relationship (QSAR/QSPR) models. These models can be used to predict the biological, physicochemical and environmental properties of chemicals.
AMBIT AMBIT is an open chemoinformatic system designed to support companies by facilitating chemical safety assessment.
Auto-QChem an automated workflow for the generation and storage of DFT calculations for organic molecules
Bioalerts Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets. (open source)
BioByte Bio-Loom has many new features, including the ability to access BioByte’s entire Thor Masterfile database of chemical properties as well as the QSAR database of Hansch equations.
BioByte Bio-Loom Bio-Loom has many new features, including the ability to access BioByte’s entire Thor Masterfile database of chemical properties as well as the QSAR database of Hansch equations.
BIOVIA COSMO-RS COSMO-RS simulations are based on a sound scientific theory, which ensures robust and reliable predictions over the whole range of chemistry in the liquid state.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
cApp cApp is a convenient and easy-to-use Java application that aids handling and storage of information about small-molecule compounds. With the application, the user can appraise compounds with respect to their physico-chemical properties and present structu
CATALOGIC The CATALOGIC software suite is a platform for models and databases related to the environment fate of chemicals such as abiotic and biotic degradation, bioaccumulation and acute aquatic toxicity.
Chainer Chemistry Chainer Chemistry is a deep learning framework (based on Chainer) with applications in Biology and Chemistry. It supports various state-of-the-art models (especially GCNN – Graph Convolutional Neural Network) for chemical property prediction.
Chemicalize Calculate properties instantly, search chemical data, and draw molecules online
Chemistry@Pirika Chemistry@Pirika is a free, browser‑based toolkit that lets you estimate thermochemical properties, polymer/Hansen‑solubility behavior, and visualize simple molecular orbitals without installing any software.
ChemmineR ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity s
ChemProp There is a public free edition based on developments within the former EU Integrated Project OSIRIS. Furthermore, there is a professional version covering all features including batch processing in terms of QSAR runs for compound lists.
Chemprop Chemprop is a repository containing message passing neural networks for molecular property prediction.
ChemPy ChemPy is a Python package useful for chemistry (mainly physical/inorganic/analytical chemistry). Currently it includes:
ChemSAR This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. I
ChemSpider ChemSpider is a free access service providing a structure centric community for chemists.
CRANIUM – Property Estimation Software Cranium is physical property estimation software package.
Danish (Q)SAR Database The Danish QSAR database has been freely available on the internet since 2004. It is a tool that allows industry, research, authorities and others to search for hazard information on chemical substances, especially those with little or no testing data
DeepChem DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.
DGL-LifeSci DGL-LifeSci is a DGL-based package for various applications in life science with graph neural networks.
EPI Suite The EPI (Estimation Programs Interface) Suite™ is a Windows®-based suite of physical/chemical property and environmental fate estimation programs developed by EPA’s and Syracuse Research Corp. (SRC).
Epik Rapid pKa and protonation state prediction tool
HazardExpert Pro HazardExpert is an ideal tool for quick prediction of compound’s toxicity in the drug discovery process or during the dispositional research phase.
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
Instant JChem Instant JChem (IJC) is an out-of-the-box tool that allows scientists to create, manage and analyze chemical structures and related non-chemical data.
KiSThelP KiSThelP – a program to predict thermodynamic properties and rate constants from quantum chemistry results.
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
Marvin The new Marvin is a universal chemical editor that serves the needs of any chemist involved in research and drug discovery.
MedChem Designer Our FREE chemical sketching software tool which combines innovative molecule drawing features with a few fast and accurate ADMET property predictions from our top-ranked ADMET Predictor software, including logP, logD(7.4), Polar Surface Area, and Lipinski
MEPS MEPS is a software developed by LMC for predicting explosive properties of chemicals in cooperation with Merck.
Millsian Millsian, Inc., is the future of molecular modeling. Utilizing a new classical approach to solving atoms and molecules, our software will help researchers design the next generation of pharmaceuticals.
MoKa MoKa implements a novel approach for in-silico computation of pKa values; trained using a very diverse set of more than 25000 pKa values.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Molinspiration – Calculation of molecular properties Calculation of molecular properties
Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
OpenChem OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend. The goal of OpenChem is to make Deep Learning models an easy-to-use tool for Computational Chemistry and Drug Design Researchers.
OrChem This project aims at creating an open source chemistry plugin / cartridge for the relational database system Oracle. Free Oracle chemistry cartridge.
OSIRIS Property Explorer The OSIRIS Property Explorer lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid.
Pallas System ADME prediction software family to boost your R&D productivity
PASS Chemo-Informatics. Compute biological activity for a compound library
pDynamo pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC),
Polymer Genome Polymer Genome is an informatics platform for PREDICTING the properties of polymers using pre-built machine learning models.
Polymer Property Predictor and Database Polymer Property Predictor and Database
PreADMET PreADMET is a web-based application for predicting ADME/Tox data and building drug-like chemical library using in silico screening method
QSAR TOOLBOX The Toolbox is a free software application that supports reproducible and transparent chemical hazard assessment.
QUACPAC QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states
RDKit RDKit: Open-Source Cheminformatics Software
SPARC ARChem’s physicochemical calculator, SPARC, uses computational algorithms based on fundamental chemical structure theory to estimate a wide variety of reactivity parameters strictly from molecular structure.
Spartan Wavefunction provides cutting edge molecular modeling software for use in research and education.
TLogP TLogP estimates logarithmic octanol/water partition coefficients (log Kow) of uncharged organic compounds.
TouchMol4Office Microsoft Office Plug-in Enabling Chemistry and Biology Functions
VCharge VCharge provides fast, easy access to accurate partial charges for virtually any drug-like compound. It is thus valuable in a wide range of modeling and QSAR applications.
VEGA QSAR Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes.
Virtual Computational Chemistry Laboratory This site provides free on-line tools, which we hope you will find helpful in performing computational chemistry, ADME/T and chemoinformatics tasks including the building and visualisation of chemical structures, the calculation of molecular properties
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.

Analytical Data Manager

a|e – UV-Vis-IR Spectral Software Software for analyzing UV-Vis absorption and emission spectra, compatible with MATLAB and Windows platforms. (freeware)
ACDLABs AutoChrom ACD/AutoChrom helps experts develop chromatographic separations using QbD principles. It uses a workflow-based structure to streamline and track a project
ACDLABs MS Workbook Suite ACD/MS Workbook Suite is an all-in-one package for MS data handling.
ACDLABs NMR Workbook Suite ACD/NMR Workbook Suite is a comprehensive NMR software application. It features a full suite of advanced processing, analysis, and databasing functionalities for 1D and 2D NMR data from all major vendor formats.
ActivityBase ActivityBase is the established industry software platform for screening data management, with feature-rich data analysis tools, built-in object/compound registration tools and the industry standard database.
alvaMolecule AlvaMolecule is a software tool to visualise, analyse, curate and standardize your molecular dataset. alvaMolecule is free for academic and non-commercial use.
CDD VAULT CDD Vault helps research teams manage, analyze, and present data, all through an intuitive user interface accessible from any web browser.
CERTARA D360 The D360 Scientific Informatics Platform is the industry-leading solution for small molecule and sequence-based modalities research, whose versatility and low total cost of ownership have made it the analysis and visualization system of choice
ChemPy ChemPy is a Python package useful for chemistry (mainly physical/inorganic/analytical chemistry). Currently it includes:
Computational Crystallography Toolbox The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system.
Crystal Studio Crystal Studio is a Windows XP/Vista/Windows 7 (32/64) /Windows 8 (32/64)/Windows 10 (32/64) and Windows 11 software package for crystallography.
CrystalDesigner CrystalDesigner is a computer program for building, studying and visualising all kinds of crystal structures
Diamond Diamond is our outstanding molecular and crystal structure visualization software.
Diversity Genie Diversity Genie™ is a powerful tool to analyze datasets of small organic molecules.
DynaFit Analysis of (bio)chemical kinetics and equilibria
EQS4WIN Chemical Equilbrium Software for Windows
Fluorescence-Tools A hub for community-driven open-source fluorescence spectroscopy software, including tools for time-resolved and steady-state fluorescence data analysis
IRPal2.0 A desktop application designed to assist in the interpretation of IR spectra, providing functional group assignments and correlation tables. (freeware)
ISOTROPY The ISOTROPY software suite is a collection of software which applies group theoretical methods to the analysis of phase transitions in crystalline solids.
Kintecus Kintecus 2025 has been released. This version can graphically display your chemical network in a myriad of ways by simple inclusion of a command line switch, “-chemnet”.
KnowItAll Analytical Edition Software Wiley’s KnowItAll provides an integrated solution to identify, analyze, and manage analytical data to accelerate your spectral analyses and increase overall lab efficiency.
LabVantage LabVantage’s AI-powered laboratory informatics platform – designed to capture lab data and put it to work for your business.
LineUp Alignment Software for Chromatography and Spectroscopy
MARS MARS (MetAbolomics ReSearch) is a vendor neutral desktop application software endowed with a Graphical User Interface (GUI) specifically developed for untargeted and semi-targeted LC-MS-based metabolomics and exposomics.
matNMR MatNMR is a highly flexible toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB
Mercury See chemistry in 3D and generate high-definition, customized images, animations, and 3D models of molecules using Mercury software.
MEXICO Suite The MEXICO Suite of Programs for NMR Chemical Exchange Lineshape Calculation
MNOVA Top-Class Software Suite for Comprehensive Analytical Chemistry Data Processing
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
molmol MOLMOL was part of a collaboration project between BRUKER/Spectrospin and Prof. Wüthrich at ETH Zürich.
Moloc a Molecular Design Software Suite
OpenLab CDS OpenLab CDS는 생산성, 유용성 및 데이터 무결성을 결합한 크로마토그래피 데이터 시스템(CDS)입니다
OpenMS OpenMS offers an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization.
Partek Flow software User-friendly bioinformatics software for the analysis and visualization of multiomic data.
PeakFit The Automatic Choice For Spectroscopy, Chromatography and Electrophoresis
PhotochemCAD PhotochemCAD™ is a program of calculational modules and accompanying database of absorption and emission spectra aimed at advancing the photosciences.
Pyxis Suite The Pyxis suite comprises a number of desktop applications for mass spectrometry imaging (MSI) data analysis, which support both untargeted and targeted data analysis, namely: Pyxis Viewer, Pyxis MSI, and Pyxis.
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
Sherlock/NMRium A Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR Data
Sigmaplot SigmaPlot Helps You Quickly Create Exact Graphs
Silk Scientific Inc. Graph Digitizing & Gel Analysis
SpecTool The comprehensive knowledge base for structure elucidation and organic spectroscopy
SpectraFit SpectraFit is a Python tool for quick data fitting based on the regular expression of distribution and linear functions via the command line (CMD) or Jupyter Notebook (open source)
SpectraGryph Easy to use. Rock solid. Lean. For UV-VIS, NIR, FTIR, Raman, fluorescence, LIBS, XRF data. Free for private & academic use.
Spectrus The Spectrus Platform is a collection of desktop software, browser-based applications, and an ecosystem of informatics technologies for handling analytical and chemical data.
Spectrus JS Spectrus JS is a family of web applications—an evolution of the tools and capabilities of the Spectrus platform.
Spotfire Only Spotfire combines visualizations and advanced analytics to allow experts in their field to find industry-specific solutions the human mind or computers can’t solve alone.
Vernier Spectral Analysis Collect, analyze, and share spectrometer data with our free app for ChromeOS™, iOS, Android™, Windows®, and macOS™.
Xtal The Xtal System is a comprehensive suite of small molecule structural solution, refinement and analysis software, supporting both X-ray, neutron and electron diffraction data.

Spectrum Prediction

ACDLABs MS Fragmenter ACD/MS Fragmenter helps you predict mass spectral fragmentation in seconds. Have more confidence in your compound IDs, learn about fragmentation mechanisms, and publish your results easily.
ACDLABs NMR Predictors From experimental design to data interpretation, ACD/Labs’ NMR predictors can significantly speed up your workflow.
BIOVIA TURBOMOLE With TURBOMOLE®, we offer a very powerful, general purpose Quantum Chemistry program package for ab initio electronic structure calculations with a very wide range of applications.
CFM-ID (MS/MS spectra prediction) his function predicts QToF MS/MS spectra for multiple collision energies for a given input small molecule.
Cheminfo IR Predictor A web-based tool that predicts IR spectra from molecular structures, allowing users to visualize and interpret vibrational modes.
CONFLEX CONFLEX permits fast, accurate, automated conformation searching and analysis critical to drug discovery and chemical engineering.
COSMOS Computer Simulation of Molecular Structures
Graphormer-IR Graphormer-IR is an extension to the Graphormer package, with documentation, and the original code on Github with additional usage examples.
IR spectra prediction in Cheminfo IR spectra prediction in Cheminfo
IR-Spectra-Prediction-Graph-Models This code was developed for use with the NIST IR spectra dataset that can be scraped by running 1) NIST Spectra Scraper.py, 2) NIST Preprocessor.ipynb, and 3) NIST Molecule Selector.ipynb in order.
JChem for Office JChem for Office integrates chemical structure handling, data analyzing, visualizing and reporting capabilities within the Microsoft Office environment.
Machine Learning Models for the Prediction of UV-Visible Spectra computational tools to devise a method for predicting accurate UV-Vis spectra to accelerate the hit identification in drug design. Below is the representation of the UVvis-MPNN model, one of the best model
Marvin The new Marvin is a universal chemical editor that serves the needs of any chemist involved in research and drug discovery.
Mass-MetaSite Mass-MetaSite is an established approach for the automatic identification of metabolites for small molecules and peptides using Liquid Chromatography – Mass Spectrometry, UV, fluorescencem, and radio-chromatogram data.
ML_UVvisModels A collection of machine learning models developed by PNNL for predicting UV-Vis spectra based on quantum mechanical calculations and experimental data
MNOVA Top-Class Software Suite for Comprehensive Analytical Chemistry Data Processing
NMR Prediction Prediction of 1H-NMR and 13C-NMR shift values based on 4000 parameters for 13C NMR and almost 3000 parameters for 1H NMR, chemical shifts are predicted using additivity rules and several strategies of approximation.
nmrdb.org This website does not contain any database of NMR spectra but allows to predict easily 13C as well as 1H spectra.
nmrshifdb2 nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra.
ORCA ORCA is a powerful and versatile quantum chemistry software package, primarily developed by the group of Prof. Frank Neese
PCmodel Serena Software announces the release of version 10.0 of Pcmodel. Completely redesigned with a new user interface, built with cross platform tools, with support Linux, Windows 10 and Mac OsX.
Q-CHEM Q-Chem is an ab initio quantum chemistry software package for fast and accurate simulations of molecular systems, including electronic and molecular structure, reactivities, properties, and spectra.
SchNarc A SchNetPack/SHARC interface for machine-learning accelerated excited state simulations.
SingleFrag (MS/MS fragment) A deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation.
UV-adVISor UV-adVISor is a machine learning model that maps SMILES to predicted wavelength spectra of a compound between 400-700nm.

Structure Elucidation

Apex The Apex software is designed to answer a simple question: Is my molecule in my sample? By comparing spectral features predicted from molecular structure with experimental MS and MS/MS data, Apex can quickly analyze entire datasets to determine which of
ARIA ARIA (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the assignment process through the use of an iterative structure calculation scheme.
CMC-se Bruker´s CMC-se Software package for simple structure elucidation, particularly small molecule elucidation.
Daylight Chemical Information Systems, Inc Daylight provides cheminformatics toolkits, applications, web services, and database systems that are infinitely customizable to accommodate the needs of a wide variety of specialized scientific applications.
Indigo Toolkit Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization.
JChem Engines Search through tens of millions of chemical compounds and receive relevant query hits in seconds.
LigPrep LigPrep is a tool to robustly and rapidly prepare high-quality small molecule ligand structures for structure-based virtual screening and other computational workflows.
LSD The aim of the LSD program is to find all possible molecular structures of an organic compound that are compatible with its spectroscopic data.
MARS MARS (MetAbolomics ReSearch) is a vendor neutral desktop application software endowed with a Graphical User Interface (GUI) specifically developed for untargeted and semi-targeted LC-MS-based metabolomics and exposomics.
MassChemSite MassChemSite is a software dedicated to the structure elucidation of organic molecules produced in chemical reactions based on High Resolution Mass Spectroscopy (HRMS).
MNOVA Top-Class Software Suite for Comprehensive Analytical Chemistry Data Processing
MOLGEN The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures.
PaDEL-APC3 A RapidMiner plugin for a fully automated and computationally efficient Pearson’s correlation change classification approach for GC/MS metabonomic data.
Pyxis Suite The Pyxis suite comprises a number of desktop applications for mass spectrometry imaging (MSI) data analysis, which support both untargeted and targeted data analysis, namely: Pyxis Viewer, Pyxis MSI, and Pyxis.
Schmarnica Database Independent Automated Structure Elucidation of Organic Molecules Based on IR, 1H NMR, 13C NMR, and MS Data
Sherlock/NMRium A Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR Data
WebCoCon A new way of doing Structure Elucidation and Discussion with NMR data, now with support for reading NMReDATA files.

Biopolymer Prediction

Abalone Abalone is designed for macromolecular simulations (proteins, DNA). It supports both explicit and implicit solvent models.
AlphaFold Server AlphaFold Server is a web-service that can generate highly accurate biomolecular structure predictions containing proteins, DNA, RNA, ligands, ions, and also model chemical modifications for proteins and nucleic acids in one platform.
Amber Amber is a suite of biomolecular simulation programs.
Barry Honig Laboratory of Molecular Biophysics PrePPI, P-HIPSTer, PrePCI, PredUs, Ska, Screen
BioPredicta BioPredicta equips the researchers to protein preparation, homology modeling, model validation and protein – ligand docking in a seamless fashion.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
CAVER CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures
CHARMM A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques
DUNBRACK LAB Our group concentrates on research in computational structural biology, including structural bioinformatics of proteins and protein complexes, protein structure prediction, molecular dynamics simulations, and deep learning neural networks.
I-TASSER I-TASSER (Iterative Threading ASSEmbly Refinement) is a hierarchical approach to protein structure prediction and structure-based function annotation.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
IntFOLD The IntFOLD Integrated Protein Structure and Function Prediction Server
LOMETS LOMETS (Local Meta-Threading Server, version 3) is a next-generation meta-server approach to template-based protein structure prediction and structure-based function annotation.
MODELLER MODELLER is used for homology or comparative modeling of protein three-dimensional structures.
ModPipe ModPipe is a completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention.
ModWeb ModWeb: A Server for Protein Structure Modeling
Molecular Function This program support HyperChem and Gaussian for Homology Modeling, Docking, QM calculation.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Moloc a Molecular Design Software Suite
MPACK MPACK (Modeling Package) is an integrated protein modeling suite that currently handles comparative and ab initio modeling procedures. T
NCBI BLAST BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Next-Gen @ BioHPC This interface serves the purpose of storing and management of various data files to be used and processed by the Next Generation Sequencing analysis tools available through BioHPC.
Partek Flow software User-friendly bioinformatics software for the analysis and visualization of multiomic data.
PIPSA (Protein Interaction Property Similarity Analysis) PIPSA may be used to compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins.
PredictProtein PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein
Prime A powerful and innovative solution for accurate protein structure prediction
ProFit ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate least squares fitting program.
ProSide ProSide is a tool which predicts protein sidechain conformation
Protein Library The Protein Library (PL) is a modular library written in C++ that provides a general toolkit to perform many protein structure and sequence calculations.
PSIPRED The PSIPRED Workbench provides a range of protein structure prediction methods. The site can be used interactively via a web browser or programmatically via our REST API.
PyRosetta PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite.
Robetta Robetta is a protein structure prediction service that is continually evaluated through CAMEO
Rosetta Commons An Innovative Model for Collaboration. Advancing biomolecular modeling tools and the diverse community of biomolecular structural modelers and designers.
RPBS Web Portal A web resource for structural bioinformatics
Spruce TK Spruce TK streamlines the preparation process by automatically breaking the system into individual biological components, adding any missing protons or residues, and it finishes by optimizing the hydrogen bond network for the entire system.
SWISS-MODEL SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the Expasy web server.
Target Informatics Platform Eidogen-Sertanty’s Target Informatics Platform (TIP) is the world’s first structural informatics system and knowledgebase that enables researchers with the ability to interrogate the druggable genome from a structural perspective.
TRAPP TRAnsient Pockets in Proteins with Druggability : Calculation Analysis of transient binding pockets and druggability indices in proteins This new version implements new features like druggability indices.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.

De Novo design

Structure Based Design

3D-e-Chem NLeSC project This project will develop technologies to improve the integration of ligand and protein data for structure-based prediction of protein-ligand selectivity and polypharmacology. The project will use KNIME Analytics Platform to integrate/
BioPharmics Fast, accurate and robust 3D modelling from small molecules to large macrocycles
BioPredicta BioPredicta equips the researchers to protein preparation, homology modeling, model validation and protein – ligand docking in a seamless fashion.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
Dockamon Engage in a comprehensive and versatile suite of structure-based drug design tools, specifically tailored for molecular docking and analysis
DockThor (web server) A Free Web Server for Protein-ligand Docking
Flare Through high-resolution 3D visualization and in-depth analysis of target structures and potential ligands, Flare enables users to optimize and prioritize new molecules efficiently and effectively
fpocket The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. (open source)
GRID GRID is a computational procedure for determining energetically favourable binding sites on molecules of known structure, known as Molecular Interaction Fields (MIFs).
LEA3D LEA3D offers a facility to screen or to design small molecules
LeView (Ligand Environment Viewer) LeView (Ligand Environment Viewer) is a Java program that can be used to generate 2D representations of ligands and their environments and binding interactions for PDB entries.
Ligand Contact Tool LCT is a tool to calculate contacts between protein and ligand atoms.
LigBuilder LigBuilder V3 is a multiple-purposed program developed for structure-based de novo drug design and optimization.
LigPlot+ LigPlot+ is a successor to our original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams.
McVol This program was developed to integrate the molecular volume, solven accessible volume an Van der Waals volume of proteins using a Monte carlo algorithm
Molecular Function This program support HyperChem and Gaussian for Homology Modeling, Docking, QM calculation.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Phase Easy-to-use pharmacophore modeling solution for ligand- and structure-based drug design
PLIP web tool Easy and fast identification of non-covalent interactions between biological macromolecules and their ligands.
PocketAnalyzerPCA PocketAnalyzerPCA combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. (open source)
POVME POVME (POcket Volume MEasurer) is a program for calculating the volumes of macromolecular (e.g. protein) binding pockets
Protein Cavity Search Software to identify cavities and crevices in proteins.
ROCS ROCS is powerful ligand-based lead discovery software that identifies potentially active leads by comparing molecules using shape and the distribution of chemical features, or color
SeeSAR SeeSAR fosters innovation during every step of your drug design process. The app includes all tools vital for handling your compounds and target structures which have been fine-tuned to the needs of any chemist.
Silicos-it We provide support in all aspects of modern computational drug design, including virtual screening, molecular dynamics applications, and state-of-the-art structure-activity machine learning models
SiteMap Fast, accurate, and intuitive binding site identification
SwissTargetPrediction This website allows you to estimate the most probable macromolecular targets of a small molecule, assumed as bioactive. The prediction is founded on a combination of 2D and 3D similarity with a library of 37 0’000 known actives on more than 3000 proteins
SZMAP/GamePlan SZMAP is OpenEye’s application to help modelers and medicinal chemists understand the role of water in molecular interactions such as ligand binding.
TexMol TexMol is a molecular visualization and computation package. It allows for quick and high quality visualization of Proteins and RNA, and reads in the PDB format.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
VSTH (web server) a user-friendly web server for structure-based virtual screening on Tianhe-2
Zodiac Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output. (open source)

Virtual Screening, Docking

3D-Dock Suite FTDock(Fourier Transform Dock), RPScore(Residue level Pair potential Score), MultiDock(Multiple copy side-chain refinement Dock)
3D-e-Chem NLeSC project This project will develop technologies to improve the integration of ligand and protein data for structure-based prediction of protein-ligand selectivity and polypharmacology. The project will use KNIME Analytics Platform to integrate/
ADplugin ADplugin is a plugin for PyMOL for interfacing with AutoDock and AutoDock Vina. (open source)
AFITT AFITT is the only software to offer a fully automatic ligand fitting process that optimizes a real-space fit to density while keeping conformational strain to a minimum.
AutoDock AutoDock is a suite of free open–source software for the computational docking and virtual screening of small molecules to macromolecular receptors. (open source)
AutoDock Vina AutoDock Vina is an entirely separate code base and approach from Autodock that was developed with a focus on runtime performance and ease of system setup. (open source)
BioPharmics Fast, accurate and robust 3D modelling from small molecules to large macrocycles
Blaze Advanced ligand-based virtual screening software to dramatically increase your wet screening hit rate at a fraction of the cost
Clusterizer-DockAccessor Clusterizer-DockAccessor are tools for accessing the quality of docking protocols. It interfaces with a number of open source and free tools.
COSMOS Computer Simulation of Molecular Structures
CSD-CrossMiner The CSD-CrossMiner software allows you to build pharmacophore queries and simultaneously mine the CSD, PDB, and your proprietary structural data.
Dockamon Engage in a comprehensive and versatile suite of structure-based drug design tools, specifically tailored for molecular docking and analysis
DockoMatic DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions. (open source)
dockstring A Python package for easy molecular docking and docking benchmarking. We can dock molecules in a few lines of code from just a SMILES string!
DockThor (web server) A Free Web Server for Protein-ligand Docking
DOVIS DOVIS is an extension of AutoDock 4.0 that provides more efficient parallelization of large virtual screening jobs. (open source)
FLAP FLAP (Fingerprints for Ligands and Proteins) provides a common reference framework for comparing molecules, using GRID Molecular Interaction Fields (MIFs).
Glide Glide is the leading industrial solution for reliable ligand-receptor docking. It augments and accelerates structure-based drug design across a range of applications, including virtual screening, binding mode prediction and interactive 3D molecular design
GOLD GOLD is a widely recognized protein–ligand docking software based on a genetic algorithm.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
LEA3D LEA3D offers a facility to screen or to design small molecules
Lig3DLens An end-to-end computational toolbox for 3D virtual screening based on shape and electrostatics similarity, utilizing RDKit for conformer generation and alignment. (open source)
LigandScout The LigandScout software suite comprises the most user friendly molecular design tools available to chemists and modelers worldwide.
LiSiCA (Ligand Similarity using Clique Algorithm) LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format.
Molecular Function This program support HyperChem and Gaussian for Homology Modeling, Docking, QM calculation.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Molegro Virtual Docker Molegro Virtual Docker is an integrated platform for predicting protein – ligand interactions.
OEDocking TK The OEDocking TK from OpenEye is a programming library that provides this core docking and scoring functionality.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
PaDEL-ADV A software to perform virtual screening using AutoDock Vina.
PAPAR PAPER performs GPU accelerated alignment of molecular shapes using Gaussian overlays. (open source)
PARADOCKS Paradocks is a tool for molecular docking with population-based metaheuristics. (open source)
Pharmer Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.
Pharmit Pharmit is a successor of Pharmer that also incorporates shape matching and energy minimization (if a receptor structure is available) as part of the screen. It is primarily intended to be used as a backend to a web service. (open source)
PharmScreen A field-based virtual screening software package designed to find candidate molecules with larger chemical diversity.
Phase Easy-to-use pharmacophore modeling solution for ligand- and structure-based drug design
PyRMD PyRMD is a Ligand-Based Virtual Screening tool written in Python powered by machine learning.
PyRx PyRx is an award-winning Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets.
RACHEL RACHEL is an all-purpose ligand refinement software package designed to combinatorially derivatize a lead compound to improve ligand-receptor binding and accelerate drug discovery.
rDock rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. (open source)
rDock – The Molecular Docking Platform rDock is a suite of tools developed and tested over a number of years initially at RiboTargets, then Vernalis, before moving more recently to the York Structural Biology Laboratory (YSBL) at the University of York
ROCS ROCS is powerful ligand-based lead discovery software that identifies potentially active leads by comparing molecules using shape and the distribution of chemical features, or color
Rosetta Commons An Innovative Model for Collaboration. Advancing biomolecular modeling tools and the diverse community of biomolecular structural modelers and designers.
SeeSAR SeeSAR fosters innovation during every step of your drug design process. The app includes all tools vital for handling your compounds and target structures which have been fine-tuned to the needs of any chemist.
Silicos-it We provide support in all aspects of modern computational drug design, including virtual screening, molecular dynamics applications, and state-of-the-art structure-activity machine learning models
smina A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
SwissDock SwissDock is a web service that predicts the molecular interactions likely to occur between a target protein and a small molecule.
SwissSimilarity This website allows you to perform ligand-based virtual screening of several libraries of small molecules using different approaches.
SZMAP/GamePlan SZMAP is OpenEye’s application to help modelers and medicinal chemists understand the role of water in molecular interactions such as ligand binding.
TexMol TexMol is a molecular visualization and computation package. It allows for quick and high quality visualization of Proteins and RNA, and reads in the PDB format.
UCSF DOCK With the release of DOCK 6, we continue to improve the algorithm’s ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility.
VDock Fast protein-ligand docking and scoring with user friendly graphical interface.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
VSFlow – Virtual Screening Workflow VSFlow is an open-source command-line tool built on top of the RDKit [1] for the ligand-based virtual screening of large compound libraries (databases).
VSTH (web server) a user-friendly web server for structure-based virtual screening on Tianhe-2
Zodiac Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output. (open source)

Chemical Drawer

ACDLABs ChemSketch ACD/ChemSketch is a molecular structure drawing application with all the reporting features you need.
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Bioclipse An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Draw BIOVIA Draw enables scientists to draw and edit complex molecules, chemical reactions and biological sequences with ease, facilitating the collaborative searching, viewing, communicating, and archiving of scientific information.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
BKChem BKChem is a free (as in free software :o) chemical drawing program.
CH5M3D This program uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules.
Chemdoodle 2D/3D Chemdoodle 2D for 2D Chemical Drawing, Publishing and Informatics, Chemdoodle 3D for 3D Chemical Graphics, Animations and Modeling
ChemDraw Since 1985 ChemDraw has provided powerful capabilities and integrations to help you quickly turn ideas & drawings into publications you can be proud of.
chemfig The package provides the command \chemfig{<code>}, which draws molecules using the TikZ package. The <code> argument provides instructions for the drawing operation.
Chemicalize Calculate properties instantly, search chemical data, and draw molecules online
Chemistry 4-D Draw Chemistry 4-D Draw is a next-generation chemistry program combining the most advanced technologies in structure drawing.
ChemPen 1.4 ChemPen is the low cost, easy to use tool for chemists, educators and students who need to create create drawings for chemical documentation.
ChemPen3D ChemPen3D is developed by ChemPen Software and is used by 1 user of Software Informer. The most popular version of this product among our users is 1.7
Chemtool Chemtool is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
ChemWindow Wiley’s KnowItAll, ChemWindow Edition is the software chemists choose for chemical structure drawing and publishing worldwide.
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
JChemPaint Chemical 2D structure editor application/applet based on the Chemistry Development Kit(open source).
JSME Molecule Editor JSME is a free molecule editor written in JavaScript. JSME is a direct successor of the JME Molecule Editor applet.
Marvin The new Marvin is a universal chemical editor that serves the needs of any chemist involved in research and drug discovery.
MedChem Designer Our FREE chemical sketching software tool which combines innovative molecule drawing features with a few fast and accurate ADMET property predictions from our top-ranked ADMET Predictor software, including logP, logD(7.4), Polar Surface Area, and Lipinski
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
MolView MolView is an application for sketching and viewing small molecular structures. You can export images and find references to chemical information.
Orion Orion® is a cloud platform for all your molecular design and simulation needs, eliminating the need to buy and maintain expensive infrastructure. No software to install, you just need a web browser.
OSIRIS Property Explorer The OSIRIS Property Explorer lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid.
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
SketchEl SketchEl is an interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.
SMARTSeditor The SMARTSeditor is a graphic editing tool for generic chemical patterns. Based on the SMARTS language, chemical patterns can be created and edited interactively, similar to molecule editing in a chemical structure editor.
TouchMol4Office Microsoft Office Plug-in Enabling Chemistry and Biology Functions
XDrawChem Files Reviews Support Mailing Lists Tickets ▾ Discussion Code GitHub XDrawChem is an application for drawing and analyzing chemical structures and reactions. Please visit the website for full details.
Xemistry Sketcher This structure sketcher and Internet structure data retrieval tool does not rely on Java, Plug-Ins or any other browser- or platform-dependent components – all intelligence is concentrated on the server and conveniently maintained there.

Chemical Visualization

3Dmol.js 3Dmol.js is an object-oriented, WebGL accelerated JavaScript library for online molecular visualization.
AIM2000 A Program to Analyse and Visualize Atoms in Molecules Version 2
ArgusLab ArgusLab is a molecular modeling, graphics, and drug design program for Windows operating systems.
Ascalaph Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations in the gas or in condensed phase. It can interact with external mole
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
BALL BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed for this purpose.
BALLVIEW BALLView is BALL’s standalone molecular modelling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.
Bioclipse An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
bodil Bodil is a modular, multi-platform software package for biomolecular visualization and modeling.
CAVER CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures
CH5M3D This program uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules.
Chemcraft Chemcraft is a graphical program for working with quantum chemistry computations.
ChemDoodle 3D 3D Chemical Graphics, Animations and Modeling or Windows, macOS and Linux
Chemis3D Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document.
Chemistry@Pirika Chemistry@Pirika is a free, browser‑based toolkit that lets you estimate thermochemical properties, polymer/Hansen‑solubility behavior, and visualize simple molecular orbitals without installing any software.
chemkit chemkit is an open source software library for chemistry applications, particularly in the areas of cheminformatics, molecular visualization and molecular modeling.
ChemPen3D ChemPen3D is developed by ChemPen Software and is used by 1 user of Software Informer. The most popular version of this product among our users is 1.7
ChemSite ChemSite ™ is a 3D molecular modeling program that allows you to model, animate, render and export 3D molecular graphics for visualization and publication.
Chimera UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments.
Cn3D Cn3D (“see in 3D”) is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI’s Entrez Structure database.
COSMOS Computer Simulation of Molecular Structures
Crystal Studio Crystal Studio is a Windows XP/Vista/Windows 7 (32/64) /Windows 8 (32/64)/Windows 10 (32/64) and Windows 11 software package for crystallography.
CueMol CueMol is a computer program for the macromolecular structure visualization (CueMol was formerly called “Que”).
DataWarrior An Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. (open source)
Diamond Diamond is our outstanding molecular and crystal structure visualization software.
DL Visualize v3.0 DLV is a graphical user interface for use with a variety of materials simulation software.
ECCD (Extensible Computational Chemistry Environment) ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze
ECCE The Extensible Computational Chemistry Environment (ECCE, pronounced “etch-ā”) provides a sophisticated graphical user interface, scientific visualization tools.
ePMV The open-source uPy plugin, embedded Python Molecular Viewer (ePMV) runs molecular-modeling software directly in several professional 3D animation applications (hosts).
Gabedit Gabedit is a graphical user interface to computational chemistry packages like deMon2k, Gamess-US, Gaussian, Molcas, Molpro, MPQC, MOPAC, Orca, PCGamess and Q-Chem
GaussView GaussView 6 is the latest iteration of a graphical interface used with Gaussian. It aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instructio
ghemical Ghemical is implemented using the C++ programming language, and it has a graphical user interface which utilizes the OpenGL graphics interface and the GTK+ multiplatform widget library.
gMol gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces.
gOpenMol gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials.
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
iMol iMol is a free molecular visualization application for Mac OS X operating system.
Indigo Toolkit Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization.
Jamberoo Jamberoo (former JMolEditor) is a library of algorithms for structural Computational Chemistry implemented in the Java programming language. The Jamberoo classes can be integrated into other Java applications.
Jmol an open-source Java viewer for chemical structures in 3D Jmol icon with features for chemicals, crystals, materials and biomolecules
JMV JMV is a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use platform neutral molecular visualization tool, which can be used standalone or integrated into other programs.
JSmol JSmol is the extension of the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) as an HTML5 JavaScript-only web app.
LeView (Ligand Environment Viewer) LeView (Ligand Environment Viewer) is a Java program that can be used to generate 2D representations of ligands and their environments and binding interactions for PDB entries.
LICSS The LICSS System (Excel-CDK) constructs a bridge between MS Excel for Windows and the Chemistry Development Kit (CDK) Java code tools enabling users to chemically enable existing spreadsheets which contain representations of chemical structures as SMILES
luscus Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. (open source)
MacroModel Versatile, full-featured molecular modeling program
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
Marvin The new Marvin is a universal chemical editor that serves the needs of any chemist involved in research and drug discovery.
Mol2Mol he current version of Mol2Mol™ recognizes, reads and writes about 50 different file formats and subformats. It contains a simple graphic display module to inspect the currently loaded molecule.
Molden Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Molecular Rift v2 Molecular Rift is a Virtual Reality Tool for Drug Designers. (open source)
MolecularGraph.jl MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.
Molegro Molecular Viewer Molegro Molecular Viewer is a free software application for visualization of molecules and Molegro Virtual Docker results.
Molekel Molekel is an open-source multi-platform molecular visualization program.
molmol MOLMOL was part of a collaboration project between BRUKER/Spectrospin and Prof. Wüthrich at ETH Zürich.
Moloc a Molecular Design Software Suite
MolView MolView is an application for sketching and viewing small molecular structures. You can export images and find references to chemical information.
MS Maestro Complete modeling environment for your materials discovery
nglview An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering.
NOC NOC (screenshots) is a free molecular explorer for protein structure visualization, validation and analysis ..
OpenAstexViewer Software for molecular visualisation.
OpenStructure Open-Source Computational Structural Biology Framework
OpenStructure Open-Source Computational Structural Biology Framework
Orion Orion® is a cloud platform for all your molecular design and simulation needs, eliminating the need to buy and maintain expensive infrastructure. No software to install, you just need a web browser.
Pharmit Pharmit is a successor of Pharmer that also incorporates shape matching and energy minimization (if a receptor structure is available) as part of the screen. It is primarily intended to be used as a backend to a web service. (open source)
PlayMolecule A web-based toolkit for visualizing molecular structures and data, integrating powerful Python libraries within the browser for enhanced capabilities.
PovChem PovChem is a chemical visualization and illustration program with a new graphic interface.
PowerMV A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
PV PV is a JavaScript viewer to visualize protein structures directly in the browsers.
PyMOL PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
PyRosetta PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite.
PyRosetta PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite.
PyVib2 PyVib2 is a program for analyzing vibrational motion and vibrational spectra, written in pure Python.
QuteMol QuteMol is an open source (GPL), interactive, high quality molecular visualization system
RasMol and OpenRasMol RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol.
RasTop RasTop is a molecular visualization software adapted from the program RasMol initially developed by Roger Sayle.
rdkit.js A powerful cheminformatics and molecule rendering toolbelt for JavaScrip
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
SCIGLASS SCIGRESS is a multiplatform molecular design, modeling and dynamics software suite designed with experimental chemists in mind.
SeeSAR SeeSAR fosters innovation during every step of your drug design process. The app includes all tools vital for handling your compounds and target structures which have been fine-tuned to the needs of any chemist.
SMARTS PLUS Create an easily interpretable visualization for your SMARTS expression. While the Compare, Search and Create functionalities are limited to SMARTS, SMARTSview handles Reaction SMILES, Reaction SMARTS, and SMIRKS.
Spartan Wavefunction provides cutting edge molecular modeling software for use in research and education.
StarDrop StarDrop™ enables a seamless flow from the latest data through predictive modelling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process.
StruMM3D StruMM3D version 9.0.0.38 is now available and has been greatly improved. The molecular recognition algorithms have been updated, the QVBMM Force Field has been tweaked to make it faster, and several new features have been introduced.
Target Informatics Platform Eidogen-Sertanty’s Target Informatics Platform (TIP) is the world’s first structural informatics system and knowledgebase that enables researchers with the ability to interrogate the druggable genome from a structural perspective.
UCSF Chimera UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments.
Unity Mol This website is about using the Unity3D game engine to create a molecular viewer, interactive simulations and serious games.
VDisplay VDisplay is a freely available 3D molecular viewer which reads the SDfiles produced by VCharge and VConf provides an easy, graphical way to view the results on a Windows computer. VDisplay can also read and display SDfiles produced by other programs.
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
VIDA visualization & communication of molecular modeling results
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
WebChemViewer Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed
WebMO WebMO is a web-based interface to computational chemistry packages.
Winmostar Accessible and straightforward front-end GUI for pre- and post-processing GAMESS, NWChem, MOPAC, LAMMPS, Gromacs and Quantum ESPRESSO.
Xtal The Xtal System is a comprehensive suite of small molecule structural solution, refinement and analysis software, supporting both X-ray, neutron and electron diffraction data.
YASARA YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux, MacOS and Android developed since 1993, that finally makes it really easy to answer your questions.
Zodiac Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output.
Zodiac Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output. (open source)

Chemical Manipulation

ActivityBase ActivityBase is the established industry software platform for screening data management, with feature-rich data analysis tools, built-in object/compound registration tools and the industry standard database.
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Bioalerts Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets. (open source)
Bioclipse An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
BioPharmics Fast, accurate and robust 3D modelling from small molecules to large macrocycles
BIOVIA Insight for Excel Scientific Data Analysis and Collaboration Within Microsoft Excel
CACTVS This page offers downloads of free academic versions of the Cactvs Chemoinformatics Toolkit.
CASE Ultra CASE Ultra is software program used in computational toxicology that identifies structural alerts related to toxicity using (Q)SAR.
CDD VAULT CDD Vault helps research teams manage, analyze, and present data, all through an intuitive user interface accessible from any web browser.
CDK (Chemistry Development Kit) The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
CGRTools Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.
chembl_beaker This is chembl_beaker package developed at ChEMBL group, EMBL-EBI, Cambridge, UK. This is wrapper for RDKit.
chemf A purely functional cheminformatics toolkit written in Scala
Chemical Identifier Resolver This service works as a resolver for different chemical structure identifiers and allows one to convert a given structure identifier into another representation or structure identifier.
Chemicalize Calculate properties instantly, search chemical data, and draw molecules online
ChemMaster Experience comprehensive and versatile cheminformatics and drug design capabilities, with a particular focus on QSAR modeling.
ChemMine ChemMine Tools: an Open Source Web Framework for Small Molecule Analysis.
ChemSAR This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. I
ChemSpiPy ChemSpiPy provides a way to interact with ChemSpider in Python. It allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.
ChemXplor ChemXplor makes it possible to study large chemical libraries, perform several types of searches to shortlist specific compounds of interest.
Cinfony Cinfony is a Python library that makes it easy to access several cheminformatics toolkits and resources.
CLIDE (Chemical Literature Data Extraction) CLIDE is a specialized software tool that harnesses advanced algorithms to trawl through scientific literature and efficiently extract relevant chemical data.
ConvertMAS ConvertMAS – molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats.
datamol Datamol is a python library to work with molecules. It’s a layer built on top of RDKit and aims to be as light as possible.
DataWarrior An Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. (open source)
Daylight Chemical Information Systems, Inc Daylight provides cheminformatics toolkits, applications, web services, and database systems that are infinitely customizable to accommodate the needs of a wide variety of specialized scientific applications.
E-BABEL E-BABEL Interactive Molecular Structure Formats Interconversion Program
Frowns Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms.
Gypsum-DL Gypsum-DL is a free, open-source program for preparing 3D small-molecule models. Beyond simply assigning atomic coordinates, Gypsum-DL accounts for alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
InChI (The IUPAC International Chemical Identifier) The IUPAC International Chemical Identifier (InChITM) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.
Indigo Toolkit Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization.
infiniSee infiniSee is your Chemical Space navigation platform to access the universe of synthetically accessible compounds.
Instant JChem Instant JChem (IJC) is an out-of-the-box tool that allows scientists to create, manage and analyze chemical structures and related non-chemical data.
JChem Engines Search through tens of millions of chemical compounds and receive relevant query hits in seconds.
JChem for Office JChem for Office integrates chemical structure handling, data analyzing, visualizing and reporting capabilities within the Microsoft Office environment.
JOELib/JOELib2 JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
Knodle KNOwledge-Driven Ligand Extractor is a software library for the recognition of atomic types, their hybridization states and bond orders in the structures of small molecules.
Leadscope Leadscope Model Applier is a powerful, easy-to-use software solution for computational toxicology, providing accurate toxicity predictions, expert review capabilities, and regulatory-ready reports in seconds.
Lexichem TK The Lexichem TK provides an efficient and highly reliable platform for the interconversion of chemical structures and chemical names.
LICSS The LICSS System (Excel-CDK) constructs a bridge between MS Excel for Windows and the Chemistry Development Kit (CDK) Java code tools enabling users to chemically enable existing spreadsheets which contain representations of chemical structures as SMILES
LigPlot+ LigPlot+ is a successor to our original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams.
MacroModel Versatile, full-featured molecular modeling program
MayaChemTools MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.
Millsian Millsian, Inc., is the future of molecular modeling. Utilizing a new classical approach to solving atoms and molecules, our software will help researchers design the next generation of pharmaceuticals.
Molecular format converter Molecular formats converter turns your files into other molecular modeling file format by on-line.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
MolecularGraph.jl MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.
MOLGEN The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures.
Moloc a Molecular Design Software Suite
MolVS MolVS is a molecule validation and standardization tool, written in Python using the RDKit chemistry framework.
Mychem Mychem is a chemoinformatics extension for MySQL.
Online SMILES Translator and Structure File Generator Online SMILES Translator and Structure File Generator
Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy
OpenMolGRID OpenMolGRID, a GRID based system for solving large-scale drug design problems.
OpenStructure Open-Source Computational Structural Biology Framework
OrChem This project aims at creating an open source chemistry plugin / cartridge for the relational database system Oracle. Free Oracle chemistry cartridge.
OSRA: Optical Structure Recognition Application OSRA is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES, or SD files – a computer recognizable molecular structure format.
PerlMol PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that “simple things should be simple”.
PreADMET PreADMET is a web-based application for predicting ADME/Tox data and building drug-like chemical library using in silico screening method
PubChemPy PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.
Pybel Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python, especially for file input/output and for accessing the attributes of atoms and molecules.
PyMOL PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
rd_filters This script provides a simple means of applying the functional group filters from the ChEMBL database, as well as a number of property filters from the RDKit, to a set of compounds.
RDKit RDKit: Open-Source Cheminformatics Software
rdkit.js A powerful cheminformatics and molecule rendering toolbelt for JavaScrip
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
SARvision | Biologics SARvision | Biologics is a desktop application that fills the gap that exists in the analysis of Biologics SAR (Sructure Activity Analysis / Sequence Activity Analysis) for peptides, RNA, protein engineering and antibody design.
SARvision|SM SARvision|SM (Small Molecules) is a desktop application to assist in the visualization, mining and organization of chemical data.
Scaffold Hunter Scaffold Hunter is a Java-based open source tool for the visual analysis of data sets with a focus on data from the life sciences, aiming at an intuitive access to large and complex data sets.
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
Silicos-it We provide support in all aspects of modern computational drug design, including virtual screening, molecular dynamics applications, and state-of-the-art structure-activity machine learning models
SMARTS PLUS Create an easily interpretable visualization for your SMARTS expression. While the Compare, Search and Create functionalities are limited to SMARTS, SMARTSview handles Reaction SMILES, Reaction SMARTS, and SMIRKS.
SMARTSeditor The SMARTSeditor is a graphic editing tool for generic chemical patterns. Based on the SMARTS language, chemical patterns can be created and edited interactively, similar to molecule editing in a chemical structure editor.
Smi2Depict Smi2Depict: Generate 2D Images from Molecule Files
Tautomerizer Tautomerizer – Predict tautomers based on 80+ rules
TouchMol4Office Microsoft Office Plug-in Enabling Chemistry and Biology Functions
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.

Chemical Similarity & Alignment

ACPC ACPC (AutoCorrelation of Partial Charges) computes ligand similarity based on a rotation and translation invariant electrostatic descriptor. (open source)
alvaDesc AlvaDesc is the next-generation tool designed for the seamless calculation of a wide range of molecular descriptors, molecular fingerprints, and user-defined structural patterns.
AMBIT AMBIT is an open chemoinformatic system designed to support companies by facilitating chemical safety assessment.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Insight for Excel Scientific Data Analysis and Collaboration Within Microsoft Excel
CDD VAULT CDD Vault helps research teams manage, analyze, and present data, all through an intuitive user interface accessible from any web browser.
CDK (Chemistry Development Kit) The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
chembl_beaker This is chembl_beaker package developed at ChEMBL group, EMBL-EBI, Cambridge, UK. This is wrapper for RDKit.
ChemDes An integrated web-based platform for molecular descriptor and fingerprint computation
chemf A purely functional cheminformatics toolkit written in Scala
chemfp chemfp is a set of command-line tools and a Python package for working with binary cheminformatics fingerprints, typically between several hundred and a few thousand bits long.
Chemicalize Calculate properties instantly, search chemical data, and draw molecules online
ChemMaster Experience comprehensive and versatile cheminformatics and drug design capabilities, with a particular focus on QSAR modeling.
ChemMine ChemMine Tools: an Open Source Web Framework for Small Molecule Analysis.
ChemmineR ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity s
ChemSpiPy ChemSpiPy provides a way to interact with ChemSpider in Python. It allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.
ChemXplor ChemXplor makes it possible to study large chemical libraries, perform several types of searches to shortlist specific compounds of interest.
Cinfony Cinfony is a Python library that makes it easy to access several cheminformatics toolkits and resources.
DataWarrior An Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. (open source)
Daylight Chemical Information Systems, Inc Daylight provides cheminformatics toolkits, applications, web services, and database systems that are infinitely customizable to accommodate the needs of a wide variety of specialized scientific applications.
Diversity Genie Diversity Genie™ is a powerful tool to analyze datasets of small organic molecules.
eiR The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.
EON EON is an electrostatics comparison program. It compares electrostatic potential maps of pre-aligned molecules and determines the Tanimoto measures for the comparison.
FastROCS FastROCSTM conducts shape searches at speeds similar to those of approximate 2D methods, like fingerprints.
fmcsR The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules
Frowns Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
Indigo Toolkit Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization.
infiniSee infiniSee is your Chemical Space navigation platform to access the universe of synthetically accessible compounds.
Instant JChem Instant JChem (IJC) is an out-of-the-box tool that allows scientists to create, manage and analyze chemical structures and related non-chemical data.
ISEFOSS ISEFOSS is a Windows 95/Windows NT based program to search for similar structures in a chemical structure database.
JChem Engines Search through tens of millions of chemical compounds and receive relevant query hits in seconds.
JChem for Office JChem for Office integrates chemical structure handling, data analyzing, visualizing and reporting capabilities within the Microsoft Office environment.
JOELib/JOELib2 JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
LICSS The LICSS System (Excel-CDK) constructs a bridge between MS Excel for Windows and the Chemistry Development Kit (CDK) Java code tools enabling users to chemically enable existing spreadsheets which contain representations of chemical structures as SMILES
LSim LSim superposes macromolecular electron densities and computes a structural similarity score.
MacroModel Versatile, full-featured molecular modeling program
MayaChemTools MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Moloc a Molecular Design Software Suite
Molpher Molpher aims to be a scalable interactive software framework to aid the exploration of the chemical space.
Mychem Mychem is a chemoinformatics extension for MySQL.
Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy
Open3DALIGN Open3DALIGN performs unsupervised rigid-body molecular alignment. (open source)
OrChem This project aims at creating an open source chemistry plugin / cartridge for the relational database system Oracle. Free Oracle chemistry cartridge.
Orion Orion® is a cloud platform for all your molecular design and simulation needs, eliminating the need to buy and maintain expensive infrastructure. No software to install, you just need a web browser.
PaDEL-Descriptor A software to calculate molecular descriptors and fingerprints. The software currently calculates 1875 descriptors (1444 1D, 2D descriptors and 431 3D descriptors) and 12 types of fingerprints (total 16092 bits).
PAPAR PAPER performs GPU accelerated alignment of molecular shapes using Gaussian overlays. (open source)
PowerMV A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
PubChemPy PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.
RDKit RDKit: Open-Source Cheminformatics Software
rdkit.js A powerful cheminformatics and molecule rendering toolbelt for JavaScrip
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
SeeSAR SeeSAR fosters innovation during every step of your drug design process. The app includes all tools vital for handling your compounds and target structures which have been fine-tuned to the needs of any chemist.
Silicos-it We provide support in all aspects of modern computational drug design, including virtual screening, molecular dynamics applications, and state-of-the-art structure-activity machine learning models
Spark Spark™ for scaffold hopping and bioisosteric replacement
SwissSimilarity This website allows you to perform ligand-based virtual screening of several libraries of small molecules using different approaches.
TouchMol4Office Microsoft Office Plug-in Enabling Chemistry and Biology Functions
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
Vrms Vrms provides the symmetry-corrected root-mean-square deviation (RMSD) between a series of test conformations of a drug-like molecule and a reference conformation.

Structure Analysis & Data Visualization

ActivityBase ActivityBase is the established industry software platform for screening data management, with feature-rich data analysis tools, built-in object/compound registration tools and the industry standard database.
alvaMolecule AlvaMolecule is a software tool to visualise, analyse, curate and standardize your molecular dataset. alvaMolecule is free for academic and non-commercial use.
AMBIT AMBIT is an open chemoinformatic system designed to support companies by facilitating chemical safety assessment.
Bioalerts Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets. (open source)
Bioclipse An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Insight for Excel Scientific Data Analysis and Collaboration Within Microsoft Excel
CACTVS This page offers downloads of free academic versions of the Cactvs Chemoinformatics Toolkit.
CDD VAULT CDD Vault helps research teams manage, analyze, and present data, all through an intuitive user interface accessible from any web browser.
CDK (Chemistry Development Kit) The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
CERTARA D360 The D360 Scientific Informatics Platform is the industry-leading solution for small molecule and sequence-based modalities research, whose versatility and low total cost of ownership have made it the analysis and visualization system of choice
chembl_beaker This is chembl_beaker package developed at ChEMBL group, EMBL-EBI, Cambridge, UK. This is wrapper for RDKit.
chemf A purely functional cheminformatics toolkit written in Scala
Chemicalize Calculate properties instantly, search chemical data, and draw molecules online
ChemMine ChemMine Tools: an Open Source Web Framework for Small Molecule Analysis.
chemmodlab chemmodlab contains a suite of methods for fitting machine learning models and for validating the resulting models.
ChemSpiPy ChemSpiPy provides a way to interact with ChemSpider in Python. It allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.
ChemXplor ChemXplor makes it possible to study large chemical libraries, perform several types of searches to shortlist specific compounds of interest.
Cinfony Cinfony is a Python library that makes it easy to access several cheminformatics toolkits and resources.
Codessa Comprehensive Descriptors for Structural and Statistical Analysis.
Danish (Q)SAR Database The Danish QSAR database has been freely available on the internet since 2004. It is a tool that allows industry, research, authorities and others to search for hazard information on chemical substances, especially those with little or no testing data
DataWarrior An Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. (open source)
Daylight Chemical Information Systems, Inc Daylight provides cheminformatics toolkits, applications, web services, and database systems that are infinitely customizable to accommodate the needs of a wide variety of specialized scientific applications.
Diversity Genie Diversity Genie™ is a powerful tool to analyze datasets of small organic molecules.
fmcsR The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules
Frowns Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
Indigo Toolkit Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization.
infiniSee infiniSee is your Chemical Space navigation platform to access the universe of synthetically accessible compounds.
Instant JChem Instant JChem (IJC) is an out-of-the-box tool that allows scientists to create, manage and analyze chemical structures and related non-chemical data.
JChem Engines Search through tens of millions of chemical compounds and receive relevant query hits in seconds.
JChem for Office JChem for Office integrates chemical structure handling, data analyzing, visualizing and reporting capabilities within the Microsoft Office environment.
JOELib/JOELib2 JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
Leadscope Leadscope Model Applier is a powerful, easy-to-use software solution for computational toxicology, providing accurate toxicity predictions, expert review capabilities, and regulatory-ready reports in seconds.
LICSS The LICSS System (Excel-CDK) constructs a bridge between MS Excel for Windows and the Chemistry Development Kit (CDK) Java code tools enabling users to chemically enable existing spreadsheets which contain representations of chemical structures as SMILES
LigandScout The LigandScout software suite comprises the most user friendly molecular design tools available to chemists and modelers worldwide.
LigPlot+ LigPlot+ is a successor to our original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams.
Lilly-Medchem-Rules his is an implementation of Eli Lilly Medchem Rules. They were published under “Rules for Identifying Potentially Reactive or Promiscuous Compounds” by Robert F. Bruns and Ian W. Watson, J. Med. Chem. 2012, 55, 9763-9772.
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
MayaChemTools MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
MolecularGraph.jl MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.
Moloc a Molecular Design Software Suite
Molpher Molpher aims to be a scalable interactive software framework to aid the exploration of the chemical space.
MolVS MolVS is a molecule validation and standardization tool, written in Python using the RDKit chemistry framework.
MoSS MoSS – Molecular Substructure Miner
MS Maestro Complete modeling environment for your materials discovery
Mychem Mychem is a chemoinformatics extension for MySQL.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy
OrChem This project aims at creating an open source chemistry plugin / cartridge for the relational database system Oracle. Free Oracle chemistry cartridge.
Orion Orion® is a cloud platform for all your molecular design and simulation needs, eliminating the need to buy and maintain expensive infrastructure. No software to install, you just need a web browser.
PeakFit The Automatic Choice For Spectroscopy, Chromatography and Electrophoresis
PowerMV A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
PubChemPy PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.
Pybel Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python, especially for file input/output and for accessing the attributes of atoms and molecules.
PyMOL PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
Pyxis Suite The Pyxis suite comprises a number of desktop applications for mass spectrometry imaging (MSI) data analysis, which support both untargeted and targeted data analysis, namely: Pyxis Viewer, Pyxis MSI, and Pyxis.
rdkit.js A powerful cheminformatics and molecule rendering toolbelt for JavaScrip
REINVENT REINVENT is a molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design, molecule optimization, and other small molecule design tasks.
rpubchem This project provides an interface to Pubchem compound and assay datasets, to allow direct access to the information without going through the XML files or the PubChem web interface
Scaffold Hunter Scaffold Hunter is a Java-based open source tool for the visual analysis of data sets with a focus on data from the life sciences, aiming at an intuitive access to large and complex data sets.
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
SeeSAR SeeSAR fosters innovation during every step of your drug design process. The app includes all tools vital for handling your compounds and target structures which have been fine-tuned to the needs of any chemist.
Sigmaplot SigmaPlot Helps You Quickly Create Exact Graphs
Spotfire Only Spotfire combines visualizations and advanced analytics to allow experts in their field to find industry-specific solutions the human mind or computers can’t solve alone.
StarDrop StarDrop™ enables a seamless flow from the latest data through predictive modelling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process.
Target Informatics Platform Eidogen-Sertanty’s Target Informatics Platform (TIP) is the world’s first structural informatics system and knowledgebase that enables researchers with the ability to interrogate the druggable genome from a structural perspective.
VIDEAN VIDEAN (Visual and Interactive Descriptor Analysis)
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
Webchem webchem is a R package to retrieve chemical information from the web. This package interacts with a suite of web APIs to retrieve chemical information.
WebChemViewer Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed
Xtal The Xtal System is a comprehensive suite of small molecule structural solution, refinement and analysis software, supporting both X-ray, neutron and electron diffraction data.

Chemical Warehouse

ActivityBase ActivityBase is the established industry software platform for screening data management, with feature-rich data analysis tools, built-in object/compound registration tools and the industry standard database.
BIOVIA CISPro BIOVIA CISPro delivers a complete and sustainable solution that allows you to utilize existing workflows, yet streamline your chemical and material inventory management processes.
BIOVIA Direct The BIOVIA Direct data cartridge, for use with the Oracle database management system, improves R&D efficiency, project team collaboration and IP management.
BIOVIA Insight BIOVIA Insight also helps users collaborate seamlessly across the enterprise and among networked partners to make fast, informed decisions as a team on how to move research projects to the next level.
BIOVIA Insight for Excel Scientific Data Analysis and Collaboration Within Microsoft Excel
cApp cApp is a convenient and easy-to-use Java application that aids handling and storage of information about small-molecule compounds. With the application, the user can appraise compounds with respect to their physico-chemical properties and present structu
CBIS (Chemical and Biological Information Systems) CBIS provides a full suite of Web-based applications for managing chemical and biological materials and data throughout their lifespan
CDD VAULT CDD Vault helps research teams manage, analyze, and present data, all through an intuitive user interface accessible from any web browser.
CERTARA D360 The D360 Scientific Informatics Platform is the industry-leading solution for small molecule and sequence-based modalities research, whose versatility and low total cost of ownership have made it the analysis and visualization system of choice
Chemistry 4-D Draw Chemistry 4-D Draw is a next-generation chemistry program combining the most advanced technologies in structure drawing.
CORINA Symphony CORINA Symphony is a cheminformatics application to manage, manipulate and profile molecular data sets for in silico discovery and optimization experiments.
DataWarrior An Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. (open source)
DiSCuS an open platform for (not only) virtual screening results management
FindMolecue Chemical Inventory Management System and Electronic Lab Notebook
Instant JChem Instant JChem (IJC) is an out-of-the-box tool that allows scientists to create, manage and analyze chemical structures and related non-chemical data.
JChem Engines Search through tens of millions of chemical compounds and receive relevant query hits in seconds.
JChem for Office JChem for Office integrates chemical structure handling, data analyzing, visualizing and reporting capabilities within the Microsoft Office environment.
LabArchives All Your Research in One ELN Easily organize, search and share your scientific data in a powerful electronic lab notebook that will help you deliver higher-quality research, faster.
Labguru Powerful Lab Management Software That DrivesResultsInsightsInnovation Streamline lab operations, improve collaboration, and reach your eureka moment faster with Labguru.
LabVantage LabVantage’s AI-powered laboratory informatics platform – designed to capture lab data and put it to work for your business.
LabWare LabWare’s Enterprise Laboratory Platform is a unique and proven suite of product capabilities that encompass LIMS (Laboratory Information Management System), ELN (Electronic Laboratory Notebook), and LES (Laboratory Execution System) in an integrated
Ligand Designer Ligand Designer provides powerful, yet easy to use 3D visualization and ligand building capability that is scientifically proven while making it fun to design ligand modifications in 2D or 3D and see how those changes are likely to impact protein-ligand c
MolCart MolCart is a chemical cartridge which allows you to store large chemical compound libraries for searching and analysis.
Moloc a Molecular Design Software Suite
myStructure mySQL db app that stores chemical structures, calc. descriptors and property values. It has a descriptor calculator and a method that filters descriptors correlated with property values.
Oniro Oniro is a web container that encapsulates a number of Molecular Discovery solutions for structure elucidation, in-silico predictions, spectral database, search and reporting that could be used in multiple fields.
OpenMolGRID OpenMolGRID, a GRID based system for solving large-scale drug design problems.
OrChem This project aims at creating an open source chemistry plugin / cartridge for the relational database system Oracle. Free Oracle chemistry cartridge.
RSpace Electronic Lab Notebook RSpace is an open-source platform that orchestrates research workflows into FAIR data management ecosystems
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
Scilligence Inventory Inventory allows for the management of unique entities, reagents, and stockroom R&D materials.
Scispot Scispot alt-ELN is the most intuitive, customizable, and integrable ELN alternative for modern wet and dry labs focused on data science.
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
TouchMol4Office Microsoft Office Plug-in Enabling Chemistry and Biology Functions
Webchem webchem is a R package to retrieve chemical information from the web. This package interacts with a suite of web APIs to retrieve chemical information.

Electronic Lab Notebook(ELN)

BIOVIA ONE Lab ELN BIOVIA has 3 different electronic lab notebooks, each with unique strengths and features. All ELNs can integrate directly with BIOVIA ONE Lab, for seamless workflows as scientists move through their activities. Each ELN is available on the cloud.
CDD VAULT CDD Vault helps research teams manage, analyze, and present data, all through an intuitive user interface accessible from any web browser.
Deltasoft Electronic Lab Notebook Our ELN is designed to capture, search, share, and analyze all experiment data within a single customizable template. Use our predefined templates, customize them, or create your own free form templates.
Dotmatics ELN The Advanced, Enterprise ELN Simplify Scientific Discovery with a Powerful Online ELN
eLabFTW (open source) A free and open source electronic lab notebook Designed by researchers, for researchers, with usability in mind. Easily keep track of experiments and collaborate with your team!
FindMolecue Chemical Inventory Management System and Electronic Lab Notebook
GENEMOD ELN Transform your laboratory’s productivity with Genemod’s Electronic Lab Notebook (ELN). Improve the management of experiments, research data, protocols, and all the essential lab documentation.
IDBS E-WorkBook IDBS E-WorkBook: powerful, flexible software combining ELN, LES and LIMS capabilities
JChem Engines Search through tens of millions of chemical compounds and receive relevant query hits in seconds.
LabArchives All Your Research in One ELN Easily organize, search and share your scientific data in a powerful electronic lab notebook that will help you deliver higher-quality research, faster.
Labguru Powerful Lab Management Software That DrivesResultsInsightsInnovation Streamline lab operations, improve collaboration, and reach your eureka moment faster with Labguru.
LabVantage LabVantage’s AI-powered laboratory informatics platform – designed to capture lab data and put it to work for your business.
LabWare LabWare’s Enterprise Laboratory Platform is a unique and proven suite of product capabilities that encompass LIMS (Laboratory Information Management System), ELN (Electronic Laboratory Notebook), and LES (Laboratory Execution System) in an integrated
opentext Electronic Lab Notebook Streamline and digitize research efforts to accelerate product collaboration and innovation
RSpace Electronic Lab Notebook RSpace is an open-source platform that orchestrates research workflows into FAIR data management ecosystems
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
Scilligence Electronic Lab Notebook Our ELN simplifies many of the tasks associated with data management, so scientists can concentrate on research and development.
SciNote SciNote is a cloud-based ELN software with lab inventory, compliance, & team management tools used by the FDA, USDA and scientists in 100+ countries.
Scispot Scispot alt-ELN is the most intuitive, customizable, and integrable ELN alternative for modern wet and dry labs focused on data science.
Signals Notebook Accelerate innovation in Pharmaceutical & Biotechnology, Chemicals & Materials, and Food, Flavor, and Fragrance with the only cloud-native Electronic Lab Notebook (ELN) that natively integrates ChemDraw™ and Spotfire®.

Laboratory Information Management System (LIMS)

Library Design

Apex The Apex software is designed to answer a simple question: Is my molecule in my sample? By comparing spectral features predicted from molecular structure with experimental MS and MS/MS data, Apex can quickly analyze entire datasets to determine which of
AutoClickChem AutoClickChem performs in silico click chemistry to generate large libraries of synthetically accessible compounds.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
ChemXplor ChemXplor makes it possible to study large chemical libraries, perform several types of searches to shortlist specific compounds of interest.
CoLibri CoLibri is a toolkit for Chemical Space exploration that transforms synthetic knowledge into Chemical Spaces, constituting huge numbers of virtual but synthetically accessible compounds.
exaScreen exaScreen : Novel synthesizable hits from a 3D limitless space
GLARE GLARE is a free software that facilitates and improves the design of chemical combinatorial libraries.
Gypsum-DL Gypsum-DL is a free, open-source program for preparing 3D small-molecule models. Beyond simply assigning atomic coordinates, Gypsum-DL accounts for alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms.
ilib diverse ilib diverse is a flexible tool for creating libraries of drug-like organic molecules suitable for rational lead structure discovery in a fast and efficient way.
infiniSee infiniSee is your Chemical Space navigation platform to access the universe of synthetically accessible compounds.
LICSS The LICSS System (Excel-CDK) constructs a bridge between MS Excel for Windows and the Chemistry Development Kit (CDK) Java code tools enabling users to chemically enable existing spreadsheets which contain representations of chemical structures as SMILES
LigandScout The LigandScout software suite comprises the most user friendly molecular design tools available to chemists and modelers worldwide.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Moloc a Molecular Design Software Suite
Molpher Molpher aims to be a scalable interactive software framework to aid the exploration of the chemical space.
Open Molecule Generator Exhaustive generation of chemical structures
OpenGrowth OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments. (open source)
OSIRIS Property Explorer The OSIRIS Property Explorer lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid.
RACHEL RACHEL is an all-purpose ligand refinement software package designed to combinatorially derivatize a lead compound to improve ligand-receptor binding and accelerate drug discovery.
SARvision | Biologics SARvision | Biologics is a desktop application that fills the gap that exists in the analysis of Biologics SAR (Sructure Activity Analysis / Sequence Activity Analysis) for peptides, RNA, protein engineering and antibody design.
SARvision|SM SARvision|SM (Small Molecules) is a desktop application to assist in the visualization, mining and organization of chemical data.
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
Shop Shop is extremely useful to guide the Scaffold Hopping procedure during the Drug Discovery process
Spark Spark™ for scaffold hopping and bioisosteric replacement
StarDrop StarDrop™ enables a seamless flow from the latest data through predictive modelling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.

Ligand Based Design

ACPC ACPC (AutoCorrelation of Partial Charges) computes ligand similarity based on a rotation and translation invariant electrostatic descriptor. (open source)
AutoClickChem AutoClickChem performs in silico click chemistry to generate large libraries of synthetically accessible compounds.
AutoGrow4 AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery.
BioPharmics Fast, accurate and robust 3D modelling from small molecules to large macrocycles
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
Flare Through high-resolution 3D visualization and in-depth analysis of target structures and potential ligands, Flare enables users to optimize and prioritize new molecules efficiently and effectively
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
Ligand Designer Ligand Designer provides powerful, yet easy to use 3D visualization and ligand building capability that is scientifically proven while making it fun to design ligand modifications in 2D or 3D and see how those changes are likely to impact protein-ligand c
LiSiCA (Ligand Similarity using Clique Algorithm) LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Open3DALIGN Open3DALIGN performs unsupervised rigid-body molecular alignment. (open source)
PAPAR PAPER performs GPU accelerated alignment of molecular shapes using Gaussian overlays. (open source)
Pharmer Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.
Pharmit Pharmit is a successor of Pharmer that also incorporates shape matching and energy minimization (if a receptor structure is available) as part of the screen. It is primarily intended to be used as a backend to a web service. (open source)
PharmScreen A field-based virtual screening software package designed to find candidate molecules with larger chemical diversity.
Phase Easy-to-use pharmacophore modeling solution for ligand- and structure-based drug design
PyRMD PyRMD is a Ligand-Based Virtual Screening tool written in Python powered by machine learning.
RACHEL RACHEL is an all-purpose ligand refinement software package designed to combinatorially derivatize a lead compound to improve ligand-receptor binding and accelerate drug discovery.
REINVENT REINVENT is a molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design, molecule optimization, and other small molecule design tasks.
ROCS ROCS is powerful ligand-based lead discovery software that identifies potentially active leads by comparing molecules using shape and the distribution of chemical features, or color
Silicos-it We provide support in all aspects of modern computational drug design, including virtual screening, molecular dynamics applications, and state-of-the-art structure-activity machine learning models
StarDrop StarDrop™ enables a seamless flow from the latest data through predictive modelling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process.
SwissBioisostere SwissBioisostere provides access to a knowledge and structural database of molecular replacements.
SwissSimilarity This website allows you to perform ligand-based virtual screening of several libraries of small molecules using different approaches.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
VSFlow – Virtual Screening Workflow VSFlow is an open-source command-line tool built on top of the RDKit [1] for the ligand-based virtual screening of large compound libraries (databases).

MM-MD-MC (Comp.Chem.)

Abalone Abalone is designed for macromolecular simulations (proteins, DNA). It supports both explicit and implicit solvent models.
Amber Amber is a suite of biomolecular simulation programs.
Amsterdam Modeling Suite computational chemistry with expert support to advance your chemistry & materials R&D
ArgusLab ArgusLab is a molecular modeling, graphics, and drug design program for Windows operating systems.
Ascalaph Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations in the gas or in condensed phase. It can interact with external mole
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
BALL BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed for this purpose.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
BOSS The BOSS program is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculation
CAMPARI Campari conducts flexible Monte Carlo sampling of biopolymers in internal coordinate space, with built-in analysis routines to estimate structural properties and support for replica exchange and Wang–Landau sampling. (open source)
CHARMM A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques
Chemdoodle 2D/3D Chemdoodle 2D for 2D Chemical Drawing, Publishing and Informatics, Chemdoodle 3D for 3D Chemical Graphics, Animations and Modeling
ChemSite ChemSite ™ is a 3D molecular modeling program that allows you to model, animate, render and export 3D molecular graphics for visualization and publication.
CHIMP CHIMP is a generic tool for the modeling of chemical phenomena. Eventually, chemical reaction modeling, molecular mechanics, and quantum mechanic modules will be implemented, along with an easy to use graphical-user interface (GUI)
COSMOS Computer Simulation of Molecular Structures
CPMD (Car-Parrinello Molecular Dynamics) The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
Desmond Desmond is a GPU-powered high-performance molecular dynamics (MD) engine for predicting bulk properties of materials,
ghemical Ghemical is implemented using the C++ programming language, and it has a graphical user interface which utilizes the OpenGL graphics interface and the GTK+ multiplatform widget library.
gOpenMol gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials.
GROMACS GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles and is a community-driven project.
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
Iphigenie The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations. (open source)
LAMMPS LAMMPS is a classical molecular dynamics code with a focus on materials modeling.
MacroModel Versatile, full-featured molecular modeling program
Maestro Maestro is Schrödinger’s streamlined portal for access to state-of-the-art predictive computational modeling and machine learning workflows for molecular discovery.
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
MCCCS Towhee Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.
MDynaMix This is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard-Jones, electrostatic, covalent bonds, angles and torsion angles potentials
Millsian Millsian, Inc., is the future of molecular modeling. Utilizing a new classical approach to solving atoms and molecules, our software will help researchers design the next generation of pharmaceuticals.
MMTK (Molecular Modelling Toolkit) The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications.
MOIL – A Public Domain Molecular Modeling Software We announce the release of a new version of the package for molecular dynamics and modeling MOIL
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Moloc a Molecular Design Software Suite
MS Maestro Complete modeling environment for your materials discovery
NAMD NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NWChem NWChem: Open Source High-Performance Computational Chemistry
OPENMD OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems.
OpenMM A high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment.
PACKMOL Initial configurations for Molecular Dynamics Simulations by packing optimization
PCmodel Serena Software announces the release of version 10.0 of Pcmodel. Completely redesigned with a new user interface, built with cross platform tools, with support Linux, Windows 10 and Mac OsX.
pDynamo pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC),
ProDy ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis.
ProtoMol ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. (open source)
ProtoMS ProtoMS is a complete Monte Carlo biomolecular simulation program which is able to perform a series of different simulations, such as relative and absolute free energy calculations and water placement with GCMC and JAWS methodology. (open source)
PUPIL PUPIL,Program for User Package Interface and Linking, is a software environment – the program – that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation
PyRosetta PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite.
QMCPACK QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code.
QSite QSite is a multi-scale simulation tool that utilizes the QM/MM method, which combines the principles of quantum mechanics and molecular mechanics.
RDKit RDKit: Open-Source Cheminformatics Software
Rosetta Commons An Innovative Model for Collaboration. Advancing biomolecular modeling tools and the diverse community of biomolecular structural modelers and designers.
SCIGLASS SCIGRESS is a multiplatform molecular design, modeling and dynamics software suite designed with experimental chemists in mind.
SIRE Sire is a molecular modelling framework that provides extensive functionality to manipulate representations of biomolecular systems. (open source)
Spartan Wavefunction provides cutting edge molecular modeling software for use in research and education.
StruMM3D StruMM3D version 9.0.0.38 is now available and has been greatly improved. The molecular recognition algorithms have been updated, the QVBMM Force Field has been tweaked to make it faster, and several new features have been introduced.
TexMol TexMol is a molecular visualization and computation package. It allows for quick and high quality visualization of Proteins and RNA, and reads in the PDB format.
Tinker Molecular Modeling The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
VM2 Comprehensive software package for molecular binding free energy calculations.
WESTPA WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis) is a high-performance Python framework for applying the weighted ensemble (WE) path sampling strategy. (open source)
YANK A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations. (open source)
Zodiac Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output. (open source)

MM-MD-MC analysis tools

AmberTools AmberTools is an open source component of the non-open source Amber package and provides a large suite of analysis programs.
Ascalaph Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations in the gas or in condensed phase. It can interact with external mole
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
COSMOS Computer Simulation of Molecular Structures
ghemical Ghemical is implemented using the C++ programming language, and it has a graphical user interface which utilizes the OpenGL graphics interface and the GTK+ multiplatform widget library.
gOpenMol gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials.
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
LOOS LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods. (open source)
lsfitpar lsfitpar derives bonded parameters for Class I force fields by performing a robust fit to potential energy scans provided by the user. (open source)
MacroModel Versatile, full-featured molecular modeling program
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
MDAnalysis MDAnalysis is a Python library for reading and analyzing molecular dynamics simulations with some time critical sections written in C. (open source)
MDTraj MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories. (open source)
MEMBPLUGIN MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the VMD) environment to analyze biomolecular simulations of lipid bilayers. (open source)
MEPSA MEPSA (Minimum Energy Pathway Analysis) provides tools for analyzing energy landscapes and pathways. (open source)
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Moloc a Molecular Design Software Suite
MS Maestro Complete modeling environment for your materials discovery
MSMBuilder MSMBuilder is an application and python library. It builds statistical models for high-dimensional time-series. (open source)
PACKMOL PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. (open source)
PCmodel Serena Software announces the release of version 10.0 of Pcmodel. Completely redesigned with a new user interface, built with cross platform tools, with support Linux, Windows 10 and Mac OsX.
PLUMED PLUMED interfaces with an assortment of molecular dynamics software packages to provide a unified interface for performing free energy calculations using methods such as metadynamics, umbrella sampling and steered MD (open source)
ProDy ProDy is a free and open-source Python package for protein structural dynamics analysis.
Pteros Pteros is a C++ library for molecular modeling. It is designed to simplify the development of custom programs and scripts for molecular modeling, analysis of molecular dynamics trajectories and implementing simulation and analysis algorithms.(open source)
PyEMMA PyEMMA is a Python library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics (MD) data. (open source)
PyRED PyRED generates RESP and ESP charges for the AMBER, CHARMM, OPLS, and Glycam and force fields. (open source)
PYTRAJ PYTRAJ is a Python interface to the cpptraj tool of AmberTools.
SCIGLASS SCIGRESS is a multiplatform molecular design, modeling and dynamics software suite designed with experimental chemists in mind.
simpletraj simpletraj is a lightweight Python library for parsing molecular dynamics trajectories. (open source)
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
WHAM WHAM (Weighted Histogram Analysis Method) calculates the potential of mean force (PMF) from umbrella sampling simulations.
Zodiac Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output. (open source)

Molecular Modeling Software

ArgusLab ArgusLab is a molecular modeling, graphics, and drug design program for Windows operating systems.
Ascalaph Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations in the gas or in condensed phase. It can interact with external mole
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
BioPharmics Fast, accurate and robust 3D modelling from small molecules to large macrocycles
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
bodil Bodil is a modular, multi-platform software package for biomolecular visualization and modeling.
BOSS The BOSS program is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculation
ChemSite ChemSite ™ is a 3D molecular modeling program that allows you to model, animate, render and export 3D molecular graphics for visualization and publication.
COSMOS Computer Simulation of Molecular Structures
ghemical Ghemical is implemented using the C++ programming language, and it has a graphical user interface which utilizes the OpenGL graphics interface and the GTK+ multiplatform widget library.
gOpenMol gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials.
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
ICM-PRO ICM-Pro is MolSoft’s Main Desktop Modeling Software
LAMMPS LAMMPS is a classical molecular dynamics code with a focus on materials modeling.
MacroModel Versatile, full-featured molecular modeling program
Maestro Maestro is Schrödinger’s streamlined portal for access to state-of-the-art predictive computational modeling and machine learning workflows for molecular discovery.
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
Millsian Millsian, Inc., is the future of molecular modeling. Utilizing a new classical approach to solving atoms and molecules, our software will help researchers design the next generation of pharmaceuticals.
MMTK (Molecular Modelling Toolkit) The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications.
MOIL – A Public Domain Molecular Modeling Software We announce the release of a new version of the package for molecular dynamics and modeling MOIL
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Moloc a Molecular Design Software Suite
MS Maestro Complete modeling environment for your materials discovery
NWChem NWChem: Open Source High-Performance Computational Chemistry
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy
OpenStructure Open-Source Computational Structural Biology Framework
Orion Orion® is a cloud platform for all your molecular design and simulation needs, eliminating the need to buy and maintain expensive infrastructure. No software to install, you just need a web browser.
PCmodel Serena Software announces the release of version 10.0 of Pcmodel. Completely redesigned with a new user interface, built with cross platform tools, with support Linux, Windows 10 and Mac OsX.
pDynamo pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC),
PyRosetta PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite.
Rosetta Commons An Innovative Model for Collaboration. Advancing biomolecular modeling tools and the diverse community of biomolecular structural modelers and designers.
SCIGLASS SCIGRESS is a multiplatform molecular design, modeling and dynamics software suite designed with experimental chemists in mind.
Spartan Wavefunction provides cutting edge molecular modeling software for use in research and education.
StruMM3D StruMM3D version 9.0.0.38 is now available and has been greatly improved. The molecular recognition algorithms have been updated, the QVBMM Force Field has been tweaked to make it faster, and several new features have been introduced.
TexMol TexMol is a molecular visualization and computation package. It allows for quick and high quality visualization of Proteins and RNA, and reads in the PDB format.
Tinker Molecular Modeling The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
VIDA visualization & communication of molecular modeling results
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
YASARA YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux, MacOS and Android developed since 1993, that finally makes it really easy to answer your questions.

Nomenclature

Optical Structure Recognition

Polymer Modeling, Material Design

Quantum Chemistry Tools

ABINIT ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials.
AMPAC AMPAC 10 is the latest and most advanced version of Semichem’s popular and industry-leading semiempirical program.
AMSOL Solvation models in quantum chemistry
Amsterdam Modeling Suite computational chemistry with expert support to advance your chemistry & materials R&D
Ascalaph Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations in the gas or in condensed phase. It can interact with external mole
Auto-QChem an automated workflow for the generation and storage of DFT calculations for organic molecules
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
BigDFT-suite The BigDFT-suite project regroups the packages which are needed to install, run and employ the BigDFT code for production calculations.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
BIOVIA TURBOMOLE With TURBOMOLE®, we offer a very powerful, general purpose Quantum Chemistry program package for ab initio electronic structure calculations with a very wide range of applications.
BOSS The BOSS program is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculation
CASTEP CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materials proprieties including energetics, structure at the atomic level, vibration
cclib cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages.
Chemcraft Chemcraft is a graphical program for working with quantum chemistry computations.
CHIMP CHIMP is a generic tool for the modeling of chemical phenomena. Eventually, chemical reaction modeling, molecular mechanics, and quantum mechanic modules will be implemented, along with an easy to use graphical-user interface (GUI)
COLUMBUS COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations.
CP2K CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. (open source)
Dalton Project From 2020 you can also script some standardized Dalton and LSDalton calculations with the “Dalton Project” Python package, and you can use new features for post-processing, for example plotting spectra from the calculated results.
DDEC chargemol Program Computing DDEC Atomic Charges
deMon2k A software package for density functional theory (DFT) calculations
DMol DMol3 is a commercial software package which uses density functional theory with a numerical radial function basis set to calculate the electronic properties of molecules, clusters, surfaces and crystalline solid materials from first principles.
ECCD (Extensible Computational Chemistry Environment) ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze
ErgoSCF ErgoSCF.org is the home of Ergo, a quantum chemistry program for large-scale self-consistent field calculations. (open source)
Firefly (PC GAMESS) Firefly (previously known as the PC GAMESS) is a freely available ab initio and DFT computational chemistry program developed to offer high performance on Intel-compatible x86, AMD64, and EM64T processors.
GAMESOL GAMESOL Home Page
GAMESS The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
Gaussian Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling.
GPAW GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). (open source)
HORTON Motivated by our frustration with the difficulty of adding new features to existing quantum chemistry programs, we decided to create our own Helpful Open-source Research TOol for N-fermion systems (HORTON). (open source)
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
Jaguar Jaguar is a well-validated, robust, high-performance quantum mechanics package that specializes in fast predictions of electronic structure and properties for molecular systems of all sizes.
JANPA JANPA is a freeware program package initially aimed at performing Natural Population Analysis – a method for partial atomic charges calculation and Natural Atomic Orbital creation. (open source)
KiSThelP KiSThelP – a program to predict thermodynamic properties and rate constants from quantum chemistry results.
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
Molcas Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists.
Molecular Function This program support HyperChem and Gaussian for Homology Modeling, Docking, QM calculation.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Molpro Molpro is a comprehensive system of ab initio programs for advanced molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from many other authors.
MOLSCAT MOLSCAT is a general-purpose package for performing non-reactive quantum scattering calculations for atomic and molecular collisions using coupled-channel methods.
MOPAC MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel’s NDDO approximation.
MPQC The Massively Parallel Quantum Chemistry (MPQC) platform is a research package for ab initio simulation of the electronic structure of molecules and periodic solids, with primary focus on many-body electronic structure methods. (open source)
MS Maestro Complete modeling environment for your materials discovery
NWChem NWChem: Open Source High-Performance Computational Chemistry
OpenMX OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. (open source)
ORCA ORCA is a powerful and versatile quantum chemistry software package, primarily developed by the group of Prof. Frank Neese
PCmodel Serena Software announces the release of version 10.0 of Pcmodel. Completely redesigned with a new user interface, built with cross platform tools, with support Linux, Windows 10 and Mac OsX.
pDynamo pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC),
PSI Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of molecular properties.
PyQuante PyQuante (Sourceforge Project Page) is an open-source suite of programs for developing quantum chemistry methods.
pyscf Python-based Simulations of Chemistry Framework (open source)
Q-CHEM Q-Chem is an ab initio quantum chemistry software package for fast and accurate simulations of molecular systems, including electronic and molecular structure, reactivities, properties, and spectra.
QMCPACK QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code.
Quantum ESPRESSO Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
QuantumATK QuantumATK atomic-scale modeling software enables large-scale and thus more realistic material simulations, integrating multiple simulation methods, ranging from ab initio DFT to semi-empirical and classical force fields analysis
RMG RMG is an Open Source computer code for electronic structure calculations and modeling of materials and molecules
Spartan Wavefunction provides cutting edge molecular modeling software for use in research and education.
SQ (Siam Quantum) Siam Quantum (SQ) is an ab initio quantum chemistry program that uses quantum mechanics to determine the total energy and wave function of molecules within the framework of Hartee-Fock, Density Function Theory, and MP2 method. (open source)
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
WEASEL WEASEL is our smart workflow driver. It fully automates quantum chemical workflows, and is used by experts and non specialists alike.
WebMO WebMO is a web-based interface to computational chemistry packages.
YAeHMOP YAeHMOP is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.

Quantum Chemistry - Analysis Visualization

Ascalaph Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations in the gas or in condensed phase. It can interact with external mole
Avogadro Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
cclib cclib provides a consistent interface for parsing and interpreting the results of a number of quantum chemistry packages. (open source)
ccwatcher ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a “Command Line Interface” to which it parses important output and plots SCF energies. (open source)
Chemcraft Chemcraft is a graphical program for working with quantum chemistry computations.
CHIMP CHIMP is a generic tool for the modeling of chemical phenomena. Eventually, chemical reaction modeling, molecular mechanics, and quantum mechanic modules will be implemented, along with an easy to use graphical-user interface (GUI)
ECCD (Extensible Computational Chemistry Environment) ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze
FragIt FragIt generates fragments of large molecules to use as input files in quantum chemistry programs that support fragment based methods. (open source)
Gabedit Gabedit is a graphical user interface to computational chemistry packages like deMon2k, Gamess-US, Gaussian, Molcas, Molpro, MPQC, MOPAC, Orca, PCGamess and Q-Chem
GaussSum GaussSum parses the output of ADF, GAMESS, GAMESS-UK, and Gaussian to extract useful information: progress of geometry optimisation, UV/IR/Raman spectra, MO contributions and more.
GaussView GaussView 6 is the latest iteration of a graphical interface used with Gaussian. It aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instructio
Geac Geac (Gaussian ESI Automated Creator) extracts data from Gaussian log files. (open source)
gOpenMol gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials.
HyperChem Hypercube, Inc. is a scientific software company, incorporated in 1985, specializing in molecular modeling software.
J-ICE J-ICE stands for Jmol interface for crystallographic and electronic properties. Is an extension of the powerful, platform independent molecular visualizer Jmol, towards crystallographic and electronic properties.
Jaguar Jaguar is a well-validated, robust, high-performance quantum mechanics package that specializes in fast predictions of electronic structure and properties for molecular systems of all sizes.
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
Molden Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
Molekel Molekel is an open-source multi-platform molecular visualization program.
MS Maestro Complete modeling environment for your materials discovery
Nancy_EX Nancy_EX post-processes Gaussian output and analyzes excited states including natural transition orbitals, detachment and attachment density matrices, and charge-transfer descriptors. (open source)
orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO, TURBOMOLE, GAMESS-US, PROAIMS/AIMPAC, and Gaussian output files. (open source)
PCmodel Serena Software announces the release of version 10.0 of Pcmodel. Completely redesigned with a new user interface, built with cross platform tools, with support Linux, Windows 10 and Mac OsX.
PUPIL (Program for User Package Interface and Linking) PUPIL,Program for User Package Interface and Linking, is a software environment – the program – that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation.
PyVib2 PyVib2 is a program for analyzing vibrational motion and vibrational spectra, written in pure Python.
QMForge QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations.
Quantum ESPRESSO Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Spartan Wavefunction provides cutting edge molecular modeling software for use in research and education.
VEGA ZZ VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses.
WebMO WebMO is a web-based interface to computational chemistry packages.
Winmostar Accessible and straightforward front-end GUI for pre- and post-processing GAMESS, NWChem, MOPAC, LAMMPS, Gromacs and Quantum ESPRESSO.
wxMacMolPlt. wxMacMolPlt is an open-source, cross-platform (Mac OS X, Linux and Windows) gui for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package.

Reactivity & Synthesis Tools

AiZynthFinder AiZynthFinder is a tool for retrosynthetic planning. The default algorithm is based on a Monte Carlo tree search that recursively breaks down a molecule to purchasable precursors.
ASKCOS Here, we have hosted a number of computational tools to assist in synthetic planning and other aspects of organic chemistry.
CGRTools Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.
Chemical.AI, At Chemical.AI, we advance retrosynthesis and molecule synthesis using AI and expert rules.
CHIMP CHIMP is a generic tool for the modeling of chemical phenomena. Eventually, chemical reaction modeling, molecular mechanics, and quantum mechanic modules will be implemented, along with an easy to use graphical-user interface (GUI)
Manifold Compound searching and retrosynthesis planning tool freely accessible to academic users, developed by PostEra
Organic Chemistry Reaction Simulator Organic chemistry reaction simulators leverage advanced machine learning algorithms to tackle complex chemical problems, particularly in organic synthesis.
ReactionCode ReactionCode: a format for reaction searching, analysis, classification, transform, and encoding/decoding
ReactionPredictor Webserver Predict reaction outcomes and mechanisms using machine learning.
Reaxys Reaxys is a web-based search and retrieval system for chemical compounds, bibliographic data and chemical reactions. It is built to support chemists in their daily work with focussed and relevant information in chemistry.
RInChI RInChI: a chemical identifier for reactions
RXN for Chemistry Predict reactions, find retrosynthesis pathways, and derive experimental procedures with RXN for Chemistry.
Summit Summit is a set of tools for optimising chemical processes. Summit uses recent advances in machine learning to make the process of reaction optimisation faster.
SynAsk (LLM model) a comprehensive organic chemistry domain-specific LLM platform developed by AIChemEco Inc.
SynPlanner SynPlanner is an open-source tool for retrosynthetic planning, designed to increase flexibility in training and developing customized retrosynthetic planning solutions from raw chemical data.
SynRoute SynRoute™ is a search engine that helps chemists discover synthesis routes for target molecules using literature based reactions and reactions predicted by artificial intelligence.
Syntheseus Syntheseus is a package for end-to-end retrosynthetic planning.
Synthia Expert-coded by chemists and engineered by computer scientists, SYNTHIA™ allows scientists to quickly discover novel pathways for new and published target molecules.

Programming Library

3Dmol.js 3Dmol.js is an object-oriented, WebGL accelerated JavaScript library for online molecular visualization.
ACPC ACPC (AutoCorrelation of Partial Charges) computes ligand similarity based on a rotation and translation invariant electrostatic descriptor. (open source)
ADplugin ADplugin is a plugin for PyMOL for interfacing with AutoDock and AutoDock Vina. (open source)
Apache Superset A modern, enterprise-ready business intelligence web application for data exploration and visualization, capable of handling large datasets. (open source)
Auto-QChem an automated workflow for the generation and storage of DFT calculations for organic molecules
AutoClickChem AutoClickChem performs in silico click chemistry to generate large libraries of synthetically accessible compounds.
AutoDock Vina AutoDock Vina is an entirely separate code base and approach from Autodock that was developed with a focus on runtime performance and ease of system setup. (open source)
AZOrange AZOrange is a customization for the open source software Orange.
Azure Machine Learning Studio A cloud-based integrated development environment from Microsoft that provides a drag-and-drop interface for building, testing, and deploying predictive analytics solutions.
BALL BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed for this purpose.
Bioalerts Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets. (open source)
Bioclipse An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
BioJava BioJava is an open-source project dedicated to providing a Java library for processing biological data.
CACTVS This page offers downloads of free academic versions of the Cactvs Chemoinformatics Toolkit.
CAMPARI Campari conducts flexible Monte Carlo sampling of biopolymers in internal coordinate space, with built-in analysis routines to estimate structural properties and support for replica exchange and Wang–Landau sampling. (open source)
cApp cApp is a convenient and easy-to-use Java application that aids handling and storage of information about small-molecule compounds. With the application, the user can appraise compounds with respect to their physico-chemical properties and present structu
cclib cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages.
CDK (Chemistry Development Kit) The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
CGRTools Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.
CH5M3D This program uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules.
Chainer Chemistry Chainer Chemistry is a deep learning framework (based on Chainer) with applications in Biology and Chemistry. It supports various state-of-the-art models (especially GCNN – Graph Convolutional Neural Network) for chemical property prediction.
chembl_beaker This is chembl_beaker package developed at ChEMBL group, EMBL-EBI, Cambridge, UK. This is wrapper for RDKit.
chemf A purely functional cheminformatics toolkit written in Scala
chemfig The package provides the command \chemfig{<code>}, which draws molecules using the TikZ package. The <code> argument provides instructions for the drawing operation.
chemfp chemfp is a set of command-line tools and a Python package for working with binary cheminformatics fingerprints, typically between several hundred and a few thousand bits long.
chemkit chemkit is an open source software library for chemistry applications, particularly in the areas of cheminformatics, molecular visualization and molecular modeling.
ChemMine ChemMine Tools: an Open Source Web Framework for Small Molecule Analysis.
ChemmineR ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity s
ChemML ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data
chemmodlab chemmodlab contains a suite of methods for fitting machine learning models and for validating the resulting models.
Chemprop Chemprop is a repository containing message passing neural networks for molecular property prediction.
ChemPy ChemPy is a Python package useful for chemistry (mainly physical/inorganic/analytical chemistry). Currently it includes:
ChemSpiPy ChemSpiPy provides a way to interact with ChemSpider in Python. It allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.
Cinfony Cinfony is a Python library that makes it easy to access several cheminformatics toolkits and resources.
CIRpy CIRpy is a Python interface for the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH.
Clusterizer-DockAccessor Clusterizer-DockAccessor are tools for accessing the quality of docking protocols. It interfaces with a number of open source and free tools.
CurlySMILES CurlySMILES stands for CURLY-encoded Smart Material Input Line EntryString. CurlySMILES is a chemical language for the specification of chemical materials and molecular structures
Dalton Project From 2020 you can also script some standardized Dalton and LSDalton calculations with the “Dalton Project” Python package, and you can use new features for post-processing, for example plotting spectra from the calculated results.
datamol Datamol is a python library to work with molecules. It’s a layer built on top of RDKit and aims to be as light as possible.
Daylight Chemical Information Systems, Inc Daylight provides cheminformatics toolkits, applications, web services, and database systems that are infinitely customizable to accommodate the needs of a wide variety of specialized scientific applications.
DDEC chargemol Program Computing DDEC Atomic Charges
DeepChem DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.
DescriptaStorus Descriptor computation(chemistry) and (optional) storage for machine learning.
DGL-LifeSci DGL-LifeSci is a DGL-based package for various applications in life science with graph neural networks.
DiSCuS an open platform for (not only) virtual screening results management
DockoMatic DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions. (open source)
dockstring A Python package for easy molecular docking and docking benchmarking. We can dock molecules in a few lines of code from just a SMILES string!
DOVIS DOVIS is an extension of AutoDock 4.0 that provides more efficient parallelization of large virtual screening jobs. (open source)
eiR The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.
ePMV The open-source uPy plugin, embedded Python Molecular Viewer (ePMV) runs molecular-modeling software directly in several professional 3D animation applications (hosts).
fmcsR The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules
Frog2 This repository contains the full source code of Frog2, a tool devoted to the 2D/3D generation of ensemble of conformations for small drug-like compounds.
Frowns Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms.
Galaxy Galaxy is a free, open-source system for analyzing data, authoring workflows, training and education, publishing tools, managing infrastructure, and more.
GAlib A C++ Library of Genetic Algorithm Components
GNU Octave Scientific Programming Language
Google Cloud Vertex AI A unified AI platform that offers tools for building, deploying, and scaling machine learning models, including support for AutoML and custom model development.
Gypsum-DL Gypsum-DL is a free, open-source program for preparing 3D small-molecule models. Beyond simply assigning atomic coordinates, Gypsum-DL accounts for alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms.
H2O.ai An open-source machine learning platform providing tools for building predictive models, including support for AutoML and deep learning.
IMSL Numerical Libraries The IMSL Numerical Libraries have been the cornerstone of high-performance and desktop computing as well as predictive analytics applications in science, technical and business environments for well over three decades.
Indigo Toolkit Indigo is a universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization.
IPAK Infometrix Product Access Kit
Iphigenie The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations. (open source)
Jamberoo Jamberoo (former JMolEditor) is a library of algorithms for structural Computational Chemistry implemented in the Java programming language. The Jamberoo classes can be integrated into other Java applications.
JChem Engines Search through tens of millions of chemical compounds and receive relevant query hits in seconds.
Jmol an open-source Java viewer for chemical structures in 3D Jmol icon with features for chemicals, crystals, materials and biomolecules
JOELib/JOELib2 JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
JSmol JSmol is the extension of the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) as an HTML5 JavaScript-only web app.
LIBSVM A Library for Support Vector Machines
Lig3DLens An end-to-end computational toolbox for 3D virtual screening based on shape and electrostatics similarity, utilizing RDKit for conformer generation and alignment. (open source)
Lilly-Medchem-Rules his is an implementation of Eli Lilly Medchem Rules. They were published under “Rules for Identifying Potentially Reactive or Promiscuous Compounds” by Robert F. Bruns and Ian W. Watson, J. Med. Chem. 2012, 55, 9763-9772.
lsfitpar lsfitpar derives bonded parameters for Class I force fields by performing a robust fit to potential energy scans provided by the user. (open source)
MATLAB MATLAB is a programming and numeric computing platform used by millions of engineers and scientists to analyze data, develop algorithms, and create models.
MayaChemTools MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.
McVol This program was developed to integrate the molecular volume, solven accessible volume an Van der Waals volume of proteins using a Monte carlo algorithm
MDAnalysis MDAnalysis is a Python library for reading and analyzing molecular dynamics simulations with some time critical sections written in C. (open source)
MDTraj MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories. (open source)
MEMBPLUGIN MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the VMD) environment to analyze biomolecular simulations of lipid bilayers. (open source)
MEPSA MEPSA (Minimum Energy Pathway Analysis) provides tools for analyzing energy landscapes and pathways. (open source)
ML_UVvisModels A collection of machine learning models developed by PNNL for predicting UV-Vis spectra based on quantum mechanical calculations and experimental data
MMTK (Molecular Modelling Toolkit) The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications.
Mol2vec an unsupervised machine learning approach to learn vector representations of molecular substructures
Molassembler A graph-based molecule construction tool supporting both organic and inorganic molecules, offering stereoisomer control and conformer generation through distance geometry methods
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
MolecularGraph.jl MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia.
Molpher Molpher aims to be a scalable interactive software framework to aid the exploration of the chemical space.
MolVS MolVS is a molecule validation and standardization tool, written in Python using the RDKit chemistry framework.
mordred-descriptor (open source) a molecular descriptor calculator
MoSS MoSS – Molecular Substructure Miner
MSMBuilder MSMBuilder is an application and python library. It builds statistical models for high-dimensional time-series. (open source)
Mychem Mychem is a chemoinformatics extension for MySQL.
myStructure mySQL db app that stores chemical structures, calc. descriptors and property values. It has a descriptor calculator and a method that filters descriptors correlated with property values.
Nextflow Nextflow enables scalable, reproducible, and portable scientific workflows for research and production use cases.
nglview An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering.
NOC NOC (screenshots) is a free molecular explorer for protein structure visualization, validation and analysis ..
Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy
Open Molecule Generator Exhaustive generation of chemical structures
Open3DALIGN Open3DALIGN performs unsupervised rigid-body molecular alignment. (open source)
Open3DGRID An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)
OpenChem OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend. The goal of OpenChem is to make Deep Learning models an easy-to-use tool for Computational Chemistry and Drug Design Researchers.
OpenGrowth OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments. (open source)
OpenMM A high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment.
OpenMS OpenMS offers an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization.
OpenStructure Open-Source Computational Structural Biology Framework
OpenStructure Open-Source Computational Structural Biology Framework
OrChem This project aims at creating an open source chemistry plugin / cartridge for the relational database system Oracle. Free Oracle chemistry cartridge.
PACKMOL PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. (open source)
PAPAR PAPER performs GPU accelerated alignment of molecular shapes using Gaussian overlays. (open source)
PARADOCKS Paradocks is a tool for molecular docking with population-based metaheuristics. (open source)
pDynamo pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC),
PerlMol PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that “simple things should be simple”.
Pharmer Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.
PLUMED PLUMED interfaces with an assortment of molecular dynamics software packages to provide a unified interface for performing free energy calculations using methods such as metadynamics, umbrella sampling and steered MD (open source)
PocketAnalyzerPCA PocketAnalyzerPCA combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. (open source)
Posit (formerly RStudio) An open-source data science platform centered around R and Python, offering tools for data analysis, visualization, and reproducible research.
POVME POVME (POcket Volume MEasurer) is a program for calculating the volumes of macromolecular (e.g. protein) binding pockets
ProDy ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis.
ProDy ProDy is a free and open-source Python package for protein structural dynamics analysis.
Protein Cavity Search Software to identify cavities and crevices in proteins.
Protein Library The Protein Library (PL) is a modular library written in C++ that provides a general toolkit to perform many protein structure and sequence calculations.
ProtoMol ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. (open source)
ProtoMS ProtoMS is a complete Monte Carlo biomolecular simulation program which is able to perform a series of different simulations, such as relative and absolute free energy calculations and water placement with GCMC and JAWS methodology. (open source)
Pteros Pteros is a C++ library for molecular modeling. It is designed to simplify the development of custom programs and scripts for molecular modeling, analysis of molecular dynamics trajectories and implementing simulation and analysis algorithms.(open source)
PubChemPy PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.
PV PV is a JavaScript viewer to visualize protein structures directly in the browsers.
Pybel Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python, especially for file input/output and for accessing the attributes of atoms and molecules.
PyChem A univariate and multivariate analysis UI. This project is no longer under development.
PyEMMA PyEMMA is a Python library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics (MD) data. (open source)
PyG (PyTorch Geometric) (PyTorch Geometric) is a library built upon PyTorch to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data.
PyMOL PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
PyRED PyRED generates RESP and ESP charges for the AMBER, CHARMM, OPLS, and Glycam and force fields. (open source)
PyRMD PyRMD is a Ligand-Based Virtual Screening tool written in Python powered by machine learning.
PyRosetta PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite.
PyRx PyRx is an award-winning Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets.
PYTRAJ PYTRAJ is a Python interface to the cpptraj tool of AmberTools.
R project R is a free software environment for statistical computing and graphics.
Rcpi Rcpi offers a molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
rd_filters This script provides a simple means of applying the functional group filters from the ChEMBL database, as well as a number of property filters from the RDKit, to a set of compounds.
RDKit RDKit: Open-Source Cheminformatics Software
rdkit.js A powerful cheminformatics and molecule rendering toolbelt for JavaScrip
rDock rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. (open source)
ReactionCode ReactionCode: a format for reaction searching, analysis, classification, transform, and encoding/decoding
rpubchem This project provides an interface to Pubchem compound and assay datasets, to allow direct access to the information without going through the XML files or the PubChem web interface
Sapio Science Platform Sapio Sciences delivers the leading AI-powered lab informatics platform, uniting LIMS, ELN, and Scientific Data Cloud advanced SDMS on a shared foundation with purpose-built solutions for scientific research, discovery, manufacturing, and clinical diagnos
Scilab Scilab is a free and open source software for engineers & scientists, with a long history (first release in 1994) and a growing community (100 000 downloads every months worldwide).
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
shape Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.
Silicos-it We provide support in all aspects of modern computational drug design, including virtual screening, molecular dynamics applications, and state-of-the-art structure-activity machine learning models
SIMCA® SIMCA® is not just for data scientists. With SIMCA® you don’t need a PhD in statistics or programming to do your own data mining, multivariate calibration and predictive modeling.
simpletraj simpletraj is a lightweight Python library for parsing molecular dynamics trajectories. (open source)
SIRE Sire is a molecular modelling framework that provides extensive functionality to manipulate representations of biomolecular systems. (open source)
Small molecule conformer generation Simple webapp to generate small ligand conformers for docking using RDKit.
SpectraFit SpectraFit is a Python tool for quick data fitting based on the regular expression of distribution and linear functions via the command line (CMD) or Jupyter Notebook (open source)
Summit Summit is a set of tools for optimising chemical processes. Summit uses recent advances in machine learning to make the process of reaction optimisation faster.
VIDEAN VIDEAN (Visual and Interactive Descriptor Analysis)
VSFlow – Virtual Screening Workflow VSFlow is an open-source command-line tool built on top of the RDKit [1] for the ligand-based virtual screening of large compound libraries (databases).
Webchem webchem is a R package to retrieve chemical information from the web. This package interacts with a suite of web APIs to retrieve chemical information.
WebChemViewer Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed
WESTPA WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis) is a high-performance Python framework for applying the weighted ensemble (WE) path sampling strategy. (open source)
WHAM WHAM (Weighted Histogram Analysis Method) calculates the potential of mean force (PMF) from umbrella sampling simulations.
YANK A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations. (open source)
Zodiac Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output. (open source)

Workflow Tools

3D-e-Chem NLeSC project This project will develop technologies to improve the integration of ligand and protein data for structure-based prediction of protein-ligand selectivity and polypharmacology. The project will use KNIME Analytics Platform to integrate/
Altair® RapidMiner® Altair RapidMiner empowers organizations to unlock data insights and harness data analytics and advanced AI automation for scalable, future-ready solutions.
Alteryx A user-friendly platform offering drag-and-drop workflows for data preparation, blending, and advanced analytics, including predictive and spatial analysis
AMBIT AMBIT is an open chemoinformatic system designed to support companies by facilitating chemical safety assessment.
Analytica A visual software for building and analyzing quantitative decision models, featuring influence diagrams and intelligent arrays for multidimensional data analysis.
Apache Superset A modern, enterprise-ready business intelligence web application for data exploration and visualization, capable of handling large datasets. (open source)
Azure Machine Learning Studio A cloud-based integrated development environment from Microsoft that provides a drag-and-drop interface for building, testing, and deploying predictive analytics solutions.
BIOVIA Pipeline Pilot Leveraging BIOVIA Pipeline Pilot and its Collections, users author data pipelines, or protocols in Pipeline Pilot, to deliver integrated, data-driven solutions, and potentially combine them with other BIOVIA applications to augment out-of-the-box capabili
ChemSAR This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. I
Dataiku A collaborative data science platform that enables users to build, deploy, and manage data, analytics, and AI projects with a focus on everyday AI applications.
Galaxy Galaxy is a free, open-source system for analyzing data, authoring workflows, training and education, publishing tools, managing infrastructure, and more.
Google Cloud Vertex AI A unified AI platform that offers tools for building, deploying, and scaling machine learning models, including support for AutoML and custom model development.
H2O.ai An open-source machine learning platform providing tools for building predictive models, including support for AutoML and deep learning.
IBM SPSS software The IBM® SPSS® software platform offers advanced statistical analysis, a vast library of machine learning algorithms, text analysis, open-source extensibility, integration with big data and seamless deployment into applications.
Knime KNIME workflows allow anyone, whether they’re a business analyst or an experienced data scientist, to harness the latest and greatest data technology through an intuitive interface.
Metabase An open-source business intelligence tool that enables users to ask questions about data and visualize results without needing to write SQL queries.
Molegro Virtual Docker Molegro Virtual Docker is an integrated platform for predicting protein – ligand interactions.
Nextflow Nextflow enables scalable, reproducible, and portable scientific workflows for research and production use cases.
Orange Open source machine learning and data visualization.
Pentaho Data Integration A comprehensive data integration and analytics platform offering ETL capabilities, data visualization, and reporting tools within a visual interface.
Posit (formerly RStudio) An open-source data science platform centered around R and Python, offering tools for data analysis, visualization, and reproducible research.
SAS® Viya From managing and preparing data, through creating and optimizing AI models, to deployment and monitoring, with SAS Viya you’ll transform raw data into trustworthy insights 4.6x faster than other commercial and noncommercial platforms.
Savant A modern data analytics platform offering visual workflows for data preparation, analysis, and collaboration, designed to handle large-scale datasets efficiently.
Spotfire Only Spotfire combines visualizations and advanced analytics to allow experts in their field to find industry-specific solutions the human mind or computers can’t solve alone.
Taverna Taverna is a domain-independent suite of tools used to design and execute data-driven workflows.
TIBCO® Statistica TIBCO® Statistica is a professional tool for data scientists, statisticians and any data analyst who needs to extract useful insights from data.
Visual Blocks for ML A Google tool that allows users to create machine learning pipelines using a visual, drag-and-drop interface, facilitating rapid prototyping without coding.
WEASEL WEASEL is our smart workflow driver. It fully automates quantum chemical workflows, and is used by experts and non specialists alike.
Weka The WEKA Workbench. Online Appendix for “Data Mining: Practical Machine Learning Tools and Techniques

QSPR & QSAR tools

3D-QSAR This new suite of web applications has been integrated into a drug design teaching course, one that provides both theoretical and practical perspectives.
ALChemy Suite The ALChemy suite is designed to face every step of the modeling process, from the features selection to the predictive model deployment.
alvaDesc AlvaDesc is the next-generation tool designed for the seamless calculation of a wide range of molecular descriptors, molecular fingerprints, and user-defined structural patterns.
alvaModel AlvaModel is a software tool to create Quantitative Structure Activity/Property Relationship (QSAR/QSPR) models. These models can be used to predict the biological, physicochemical and environmental properties of chemicals.
alvaRunner AlvaRunner is a software tool to apply Quantitative Structure Activity/Property Relationship (QSAR/QSPR) regression and classification models on a set of molecules.
AMEDEO AMEDEO is a decision support systems that employs artificial intelligence and machine learning to explore pharmacological properties and Structure/Sequence activities of the molecules in your medicinal chemistry project
AZOrange AZOrange is a customization for the open source software Orange.
BioByte Bio-Loom has many new features, including the ability to access BioByte’s entire Thor Masterfile database of chemical properties as well as the QSAR database of Hansch equations.
BioByte Bio-Loom Bio-Loom has many new features, including the ability to access BioByte’s entire Thor Masterfile database of chemical properties as well as the QSAR database of Hansch equations.
BIOVIA Discovery Studio BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment.
BIOVIA Materials Studio BIOVIA Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and b
Chainer Chemistry Chainer Chemistry is a deep learning framework (based on Chainer) with applications in Biology and Chemistry. It supports various state-of-the-art models (especially GCNN – Graph Convolutional Neural Network) for chemical property prediction.
ChemDes An integrated web-based platform for molecular descriptor and fingerprint computation
ChemMaster Experience comprehensive and versatile cheminformatics and drug design capabilities, with a particular focus on QSAR modeling.
ChemML ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data
chemmodlab chemmodlab contains a suite of methods for fitting machine learning models and for validating the resulting models.
ChemProp There is a public free edition based on developments within the former EU Integrated Project OSIRIS. Furthermore, there is a professional version covering all features including batch processing in terms of QSAR runs for compound lists.
Chemprop Chemprop is a repository containing message passing neural networks for molecular property prediction.
ChemSAR This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. I
Codessa Comprehensive Descriptors for Structural and Statistical Analysis.
CORAL-QSAR/QSPR CORAL software/databases: QSPR/QSAR analysis for substances represented by Simplified Molecular Input-Line Entry System (SMILES) by the Monte Carlo method.
Danish (Q)SAR Database The Danish QSAR database has been freely available on the internet since 2004. It is a tool that allows industry, research, authorities and others to search for hazard information on chemical substances, especially those with little or no testing data
DataWarrior An Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. (open source)
DeepAutoQSAR Automated, scalable solution for the training and application of predictive machine learning models Request a Demo
DeepChem DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.
DescriptaStorus Descriptor computation(chemistry) and (optional) storage for machine learning.
DGL-LifeSci DGL-LifeSci is a DGL-based package for various applications in life science with graph neural networks.
Diversity Genie Diversity Genie™ is a powerful tool to analyze datasets of small organic molecules.
DMax Intelligent stand for exploring schemes of cross biological, chemical and clinical domains.
DOMAIN MANAGER The ” Domain Manager” is a software tool developed for automatic extraction of a features from training set molecules used for QSAR modelling purpose.
ERKALE ERKALE is a quantum chemistry program used to solve the electronic structure of atoms, molecules and molecular clusters. (open source)
Flare Through high-resolution 3D visualization and in-depth analysis of target structures and potential ligands, Flare enables users to optimize and prioritize new molecules efficiently and effectively
GUSAR Create quantitative models on structure-activity (structure-property) relationships
LQTA-QSAR 4D-QSAR Free Package
MAPS Platform MAPS is a modeling platform with state-of-the-art user-friendly graphical interface for model building of any types of materials ,properties simulation and powerful analysis capability
MMTK (Molecular Modelling Toolkit) The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications.
Mol2vec an unsupervised machine learning approach to learn vector representations of molecular substructures
Molconn-Z Molconn-Z is the standard program for generation of Molecular Connectivity, Shape, and Information Indices for Quantitative Structure Activity Relationship (QSAR) Analyses.
Mold2 Free software for fast-calculating descriptors from a two-dimensional chemical structure that is suitable for small and large datasets
MOLECULAR OPERATING ENVIRONMENT Molecular Operating Environment (MOE) is a comprehensive system that integrates visualization, molecular modeling, protein modeling, and method development.
MOLGEN The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures.
MolSig This project is about an algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure, based on our previously introduced signature molecular descriptor.
mordred-descriptor (open source) a molecular descriptor calculator
myStructure mySQL db app that stores chemical structures, calc. descriptors and property values. It has a descriptor calculator and a method that filters descriptors correlated with property values.
Open Drug Discovery Toolkit (ODDT) Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
Open3DGRID An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)
Open3DQSAR Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).
OpenChem OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend. The goal of OpenChem is to make Deep Learning models an easy-to-use tool for Computational Chemistry and Drug Design Researchers.
OpenMolGRID OpenMolGRID, a GRID based system for solving large-scale drug design problems.
OrChem This project aims at creating an open source chemistry plugin / cartridge for the relational database system Oracle. Free Oracle chemistry cartridge.
PaDEL-Descriptor A software to calculate molecular descriptors and fingerprints. The software currently calculates 1875 descriptors (1444 1D, 2D descriptors and 431 3D descriptors) and 12 types of fingerprints (total 16092 bits).
PASS Chemo-Informatics. Compute biological activity for a compound library
Pentacle Pentacle is an advanced software tool for obtaining alignment-independent 3D quantitative structure-activity relationships.
PharmQSAR A new state-of-the-art 3D Quantitative Structure-Activity Relationship (QSAR) software package that builds statistical models (CoMFA, CoMSIA and HyPhar) based on data obtained from experimental assays.
Pirouette Pirouette – Comprehensive Chemometrics Modeling Software
PowerMV A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
QSAR DataBase FAIR repository of (Q)SAR/QSPR models for citing and predicting
QSAR Flex One program with multiple in silico tools for approaching complex risk assessments using a weight of evidence approach
QSAR Model Development Using DTC Lab. Software Tools QSAR Model Development Using DTC Lab. Software Tools
QSAR TOOLBOX The Toolbox is a free software application that supports reproducible and transparent chemical hazard assessment.
QSAR-Co QSAR-Co software is an open source standalone tool, which is designed to develop robust classification-based QSAR models.
QSAR-Co-X (open source) an open source toolkit for multitarget QSAR modelling
QSAR4U This web-site was created to share some developments in chemoinformatics tools which can be useful for chemoinformaticians as well as for medicinal chemists and other specialists. It contains tools and approaches which were developed in collaboration with
QSARINS-Chem QSARINS-Chem standalone version software: Insubria datasets and models
QSARpro QSARpro is the most comprehensive and powerful product for the indirect approach to drug design using QSAR.
QUEEN QUEEN (QSAR Under Effective and Efficient Neural-Networks) is a product designed to automate construction, training, and deployment of predictive models for QSAR/QSPR (Quantitative Structure–Activity/Property Relationship) applications.
Rcpi Rcpi offers a molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
RDKit RDKit: Open-Source Cheminformatics Software
SCIGLASS SCIGRESS is a multiplatform molecular design, modeling and dynamics software suite designed with experimental chemists in mind.
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
StarDrop StarDrop™ enables a seamless flow from the latest data through predictive modelling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process.
ToMoCoMD-CARDD ToMoCoMD-CARDD is an interactive and user-friendly free multi-platform framework designed to calculate 2/3-D numerical descriptors (indices) for molecular structures, with the objective of characterizing or discriminating among them.
VEGA QSAR Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes.
Virtual Computational Chemistry Laboratory This site provides free on-line tools, which we hope you will find helpful in performing computational chemistry, ADME/T and chemoinformatics tasks including the building and visualisation of chemical structures, the calculation of molecular properties
VLifeMDS VLifeMDS is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms.
VolSurf+ VolSurf+ creates 128 molecular descriptors from 3D Molecular Interaction Fields (MIFs) produced by our software GRID, which are particularly relevant to ADME prediction and are also simple to interpret.

Statistics & Machine Learning Tools

Altair® RapidMiner® Altair RapidMiner empowers organizations to unlock data insights and harness data analytics and advanced AI automation for scalable, future-ready solutions.
Analyse-it The leading software for statistical analysis and method validation in Microsoft Excel
Analytic Solver Analytic Solver – Augment Excel with Decision Intelligence
Analytica A visual software for building and analyzing quantitative decision models, featuring influence diagrams and intelligent arrays for multidimensional data analysis.
Aspen Unscrambler Improve and optimize product quality, even at the molecular level.
AZOrange AZOrange is a customization for the open source software Orange.
Azure Machine Learning Studio A cloud-based integrated development environment from Microsoft that provides a drag-and-drop interface for building, testing, and deploying predictive analytics solutions.
Bayesian Network Software Packages This website contains several list of Bayesian Network Software.
Chainer Chemistry Chainer Chemistry is a deep learning framework (based on Chainer) with applications in Biology and Chemistry. It supports various state-of-the-art models (especially GCNN – Graph Convolutional Neural Network) for chemical property prediction.
ChemMaster Experience comprehensive and versatile cheminformatics and drug design capabilities, with a particular focus on QSAR modeling.
ChemML ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data
Chemprop Chemprop is a repository containing message passing neural networks for molecular property prediction.
ChemSAR This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. I
Codessa Comprehensive Descriptors for Structural and Statistical Analysis.
Databionic ESOM Tools The Databionic ESOM Tools is a suite of programs to perform data mining tasks like clustering, visualization, and classification with Emergent Self-Organizing Maps (ESOM).
DataLab DataLab is a simple to use statistics package running under Windows offering a well-balanced mixture of data editing capabilities, visualization methods and mathematical and statistical procedures.
DeepChem DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.
DGL-LifeSci DGL-LifeSci is a DGL-based package for various applications in life science with graph neural networks.
GAlib A C++ Library of Genetic Algorithm Components
Google Cloud Vertex AI A unified AI platform that offers tools for building, deploying, and scaling machine learning models, including support for AutoML and custom model development.
H2O.ai An open-source machine learning platform providing tools for building predictive models, including support for AutoML and deep learning.
IBM SPSS software The IBM® SPSS® software platform offers advanced statistical analysis, a vast library of machine learning algorithms, text analysis, open-source extensibility, integration with big data and seamless deployment into applications.
IPAK Infometrix Product Access Kit
JMP Statistical software for dynamic data exploration
Knime KNIME workflows allow anyone, whether they’re a business analyst or an experienced data scientist, to harness the latest and greatest data technology through an intuitive interface.
Kodemetrics Kodemetrics is the tool that enables exploratory and predictive statistical analysis and experimental design generation (DoE) without the need to know a specific programming language.
LIBSVM A Library for Support Vector Machines
Mathematica Mathematica는 지난 30여년 이상에 걸쳐 최신 기술 계산을 규정하고 전세계의 개발자, 교육자, 학생 등 수백만 명의 사용자에게 주요한 계산 환경을 제공해 왔습니다.
MATLAB MATLAB is a programming and numeric computing platform used by millions of engineers and scientists to analyze data, develop algorithms, and create models.
MiningMart a graphical tool for data preprocessing and mining on relational databases; supports development, documentation, re-use and exchange of complete KDD processes. Free for non-commercial purposes.
Minitab Visualize, analyze, and harness the power of your data to solve your toughest business challenges from anywhere on the cloud.
OpenChem OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend. The goal of OpenChem is to make Deep Learning models an easy-to-use tool for Computational Chemistry and Drug Design Researchers.
OpenMolGRID OpenMolGRID, a GRID based system for solving large-scale drug design problems.
Orange Open source machine learning and data visualization.
OriginLab The ultimate software for graphing & analysis
Partek Flow software User-friendly bioinformatics software for the analysis and visualization of multiomic data.
Pirouette Pirouette – Comprehensive Chemometrics Modeling Software
PowerMV A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
PyChem A univariate and multivariate analysis UI. This project is no longer under development.
PyG (PyTorch Geometric) (PyTorch Geometric) is a library built upon PyTorch to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data.
R project R is a free software environment for statistical computing and graphics.
SAS® Viya From managing and preparing data, through creating and optimizing AI models, to deployment and monitoring, with SAS Viya you’ll transform raw data into trustworthy insights 4.6x faster than other commercial and noncommercial platforms.
ScreeningAssistant 2 ScreeningAssistant 2 (SA2) is a free and open-source software that can be used to perform various simple as well as advanced chemoinformatics analysis around chemical libraries.
SIMCA® SIMCA® is not just for data scientists. With SIMCA® you don’t need a PhD in statistics or programming to do your own data mining, multivariate calibration and predictive modeling.
Spotfire Only Spotfire combines visualizations and advanced analytics to allow experts in their field to find industry-specific solutions the human mind or computers can’t solve alone.
StarProbe Enterprise data mining and intelligent analytic tools
Summit Summit is a set of tools for optimising chemical processes. Summit uses recent advances in machine learning to make the process of reaction optimisation faster.
SYSTAT Simplify your research and enhance your publications with SYSTAT’s comprehensive suite of statistical functions and brilliant 2D and 3D charts and graphs.
Tanagra TANAGRA, offers a GUI interface and methods for data access, statistics, feature selection, classification, clustering, visualization, association and more.
The Gnome Data Mine The gnome-datamine-tools is a growing collection of tools packaged to provide a freely available single collection of data mining tools.
TIBCO® Statistica TIBCO® Statistica is a professional tool for data scientists, statisticians and any data analyst who needs to extract useful insights from data.
Virtual Computational Chemistry Laboratory This site provides free on-line tools, which we hope you will find helpful in performing computational chemistry, ADME/T and chemoinformatics tasks including the building and visualisation of chemical structures, the calculation of molecular properties
Visual Blocks for ML A Google tool that allows users to create machine learning pipelines using a visual, drag-and-drop interface, facilitating rapid prototyping without coding.
Weka The WEKA Workbench. Online Appendix for “Data Mining: Practical Machine Learning Tools and Techniques

Software link

alfasoft Software and Services for Science and Development
Awesome Cheminformatics A curated list of awesome Cheminformatics software, resources, and libraries. Mostly command line based, and free or open-source. Please feel free to contribute !
ChemDB Cheminformatics Portal ChemDB Cheminformatics Portal
Click2Drug (Directory of CADD) Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services.
Fluorescence-Tools A hub for community-driven open-source fluorescence spectroscopy software, including tools for time-resolved and steady-state fluorescence data analysis
Genamics SoftwareSeek Genamics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry.
KIMHUA (김화기술) 김화기술은 최신의 시뮬레이션 포스트 프로세싱과 AI 엔지니어링 프로그램으로 기업과 학교의 연구개발에 필요한 최적화된 솚루션을 제안합니다.
Macs in Chemistry A site for chemists using Macs in Chemistry
Open Source Molecular Modeling Here we maintain an updateable catalog of open source molecular modeling software, initially taken from our paper.
OpenScience Project Open source scientific software
RPBS Web Portal A web resource for structural bioinformatics
Software tools for chemistry There are many software that are helpful for the amateur chemist, some professional, others more accessible.
Software-Related Sites in CCL.net This site show lists that are related to software that may be of interest to computational chemists.
T&J Tech inc. (주)티앤제이테크는 1996년 1월 신약개발연구분야 및 계산화학분야에 이용되는 Computer Software의 국내 보급을 시작으로 설립되어 생명공학, 생화학, 분석화학, 유기화학 및 임상의학에 이르기까지 국내의 화학과 바이오 산업에 관계된 다양한 분야에서 일익을 담당하여 왔습니다.
The OpenScience Project The OpenScience project is dedicated to writing and releasing free and Open Source scientific software.
바이텍켐스 바이텍켐스는 국내 최초로 분자모델링 소프트웨어를 도입/소개 하였으며 화학정보학, 생물정보학분야의 전세계 유수의 기업들이 사용하는 솔루션을 선정하여 국내에 공급하고 있습니다.
시그마소프트 시그마소프트는 기업,관공서,대학교,병원등의 부설연구소에서 사용하는 외산 연구용 소프트웨어의 전문판매점입니다

Cheminfomatics & Molecular Modeling Sites

3D Structure Conformer Generation

ADME/PK prediction

Toxicity prediction

Properties Prediction

Analytical Data Manager

Spectrum Prediction

Structure Elucidation

Biopolymer Prediction

De Novo design

Structure Based Design

Virtual Screening, Docking

Chemical Drawer

Chemical Visualization

Chemical Manipulation

Chemical Similarity & Alignment

Structure Analysis & Data Visualization

Chemical Warehouse

Electronic Lab Notebook(ELN)

Laboratory Information Management System (LIMS)

Library Design

Ligand Based Design

MM-MD-MC (Comp.Chem.)

MM-MD-MC analysis tools

Molecular Modeling Software

Nomenclature

Optical Structure Recognition

Polymer Modeling, Material Design

Quantum Chemistry Tools

Quantum Chemistry - Analysis Visualization

Reactivity & Synthesis Tools

Programming Library

Workflow Tools

QSPR & QSAR tools

Statistics & Machine Learning Tools

Software link

Chemical Education

Documentation, DB tools