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)