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Awesome Cheminformatics – Massive Collection of Resources

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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.




  • 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


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

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.

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
  • ChemML – ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
  • OpenChem – OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.
  • 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.

Web APIs


  • razi – Cheminformatic extension for the SQLAlchemy database.


  • Rosetta – A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.

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.







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