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.
  • 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.


  • 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.

Format Checking

  • standardiser - Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.
  • MolVS - Molecule validation and standardization based on RDKit.
  • rd_filters - A script to run structural alerts using the RDKit and ChEMBL


  • 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.

Molecular Descriptors

  • mordred - Molecular descriptor calculator based on RDKit.
  • 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
  • chainer-chemistry - A Library for Deep Learning in Biology and Chemistry.
  • pytorch-geometric - A PyTorch library provides implementation of many graph convolution algorithms.

Web APIs


  • razi - Cheminformatic extension for the SQLAlchemy database.

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.
  • MDTraj - Analysis of molecular dynamics trajectories.
  • cclib - Parsers and algorithms for computational chemistry logfiles.






See Also