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Awesome Cheminformatics Awesome

Cheminformatics (also known as chemoinformatics, chemioinformatics and chemical informatics) is the use of computer and informational techniques applied to a range of problems in the field of chemistry.— Wikipedia

A curated list of awesome Cheminformatics software, resources, and libraries. Mostly command line based, and free or open-source. Please feel free to contribute !




  • PyMOL - Python-enhanced molecular graphics tool.
  • Jmol - Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D.
  • VMD - Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
  • Chimera - Highly extensible program for interactive molecular visualization and analysis. Source is available.
  • ChimeraX - The next-generation molecular visualization program, following UCSF Chimera. Source is available here.
  • DataWarrior - A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.

Command Line Tools

  • Open Babel - Chemical toolbox designed to speak the many languages of chemical data.
  • MayaChemTools - Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs.
  • Packmol - Initial configurations for molecular dynamics simulations by packing optimization.
  • BCL::Commons


  • AutoDock Vina - Molecular docking and virtual screening.
  • smina - Customized AutoDock Vina to better support scoring function development and high-performance energy minimization.

Virtual Machine

  • myChEMBL - A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)
  • 3D e-Chem Virtual Machine - Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows


General Purpose

  • RDKit - Collection of cheminformatics and machine-learning software written in C++ and Python.
  • Indigo - Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.
  • CDK (Chemistry Development Kit) - Algorithms for structural chemo- and bioinformatics, implemented in Java.
  • ChemmineR - Cheminformatics package for analyzing drug-like small molecule data in R.
  • ChemPy - A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
  • MolecularGraph.jl - A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
  • datamol: - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
  • CGRtools - Toolkit for processing molecules, reactions and condensed graphs of reactions. Can be used for chemical standardization, MCS search, tautomers generation with backward compatibility to RDKit and NetworkX.

Format Checking


  • Kekule.js - Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
  • 3Dmol.js - An object-oriented, webGL based JavaScript library for online molecular visualization.
  • JChemPaint - Chemical 2D structure editor application/applet based on the Chemistry Development Kit.
  • rdeditor - Simple RDKit molecule editor GUI using PySide.
  • nglviewer - Interactive molecular graphics for Jupyter notebooks.
  • RDKit.js - Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.

Molecular Descriptors

  • mordred - Molecular descriptor calculator based on RDKit.
  • DescriptaStorus - Descriptor computation(chemistry) and (optional) storage for machine learning.
  • mol2vec - Vector representations of molecular substructures.
  • Align-it - Align molecules according their pharmacophores.
  • Rcpi - R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.

Machine Learning

  • DeepChem - Deep learning library for Chemistry based on Tensorflow
  • Chemprop - Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
  • ChemML - ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
  • olorenchemengine - Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.
  • OpenChem - OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.
  • DGL-LifeSci - DGL-LifeSci is a DGL-based package for various applications in life science with graph neural network.
  • chainer-chemistry - A Library for Deep Learning in Biology and Chemistry.
  • pytorch-geometric - A PyTorch library provides implementation of many graph convolution algorithms.
  • chemmodlab - A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.
  • Summit - A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).

Web APIs



  • Rosetta - A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.
  • DOCKSTRING - Automates and standardizes ligand preparation for AutoDock Vina.

Molecular Dynamics

  • Gromacs - Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
  • OpenMM - High performance toolkit for molecular simulation including extensive language bindings for Python, C, C++, and even Fortran.
  • NAMD - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
  • MDTraj - Analysis of molecular dynamics trajectories.
  • cclib - Parsers and algorithms for computational chemistry logfiles.
  • ProDy - A Python package for protein dynamics analysis


  • eiR - Accelerated similarity searching of small molecules
  • OPSIN - Open Parser for Systematic IUPAC nomenclature
  • Cookiecutter for Computational Molecular Sciences - Python-centric Cookiecutter for Molecular Computational Chemistry Packages by MolSSL
  • Auto-QChem - an automated workflow for the generation and storage of DFT calculations for organic molecules.
  • Gypsum-DL - a program for converting 2D SMILES strings to 3D models.
  • RDchiral - Wrapper for RDKit's RunReactants to improve stereochemistry handling
  • confgen - Webapp for generating conformers






See Also




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