Libraries / Machine Learning

• Chemprop (⭐1.5k) - Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.

Libraries / Docking

• DOCKSTRING (⭐121) - Automates and standardizes ligand preparation for AutoDock Vina.

Libraries / Web APIs

• ambit - offers chemoinformatics functionality via REST web services.

Libraries / Databases

• Chemical Translation Service - Source code of the Chemical Translation Service web service.

Libraries / Molecular Dynamics

• ProDy (⭐379) - A Python package for protein dynamics analysis

Libraries / Others

• Gypsum-DL - a program for converting 2D SMILES strings to 3D models.

• RDchiral (⭐144) - Wrapper for RDKit's RunReactants to improve stereochemistry handling

• confgen (⭐4) - Webapp for generating conformers

See Also / Books

• awesome-molecular-docking (⭐80) - A curated list of molecular docking software, datasets, and other closely related resources.

Libraries / Machine Learning

• DGL-LifeSci (⭐667) - DGL-LifeSci is a DGL-based package for various applications in life science with graph neural network.

Libraries / Machine Learning

• olorenchemengine (⭐95) - Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.

Libraries / Others

• Auto-QChem (⭐71) - an automated workflow for the generation and storage of DFT calculations for organic molecules.

Libraries / General Purpose

• CGRtools (⭐38) - 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.

See Also / Books

• awesome-small-molecule-ml (⭐168) - A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.

Libraries / Format Checking

• pdb-tools (⭐344) - A swiss army knife for manipulating and editing PDB files.

Resources / Blogs

• Cheminformania - Blog of Ph.D, Esben Jannik Bjerrum, who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.

Libraries / General Purpose

• datamol (⭐417): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.

Libraries / Visualization

• RDKit.js - Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.

Libraries / Machine Learning

• Summit (⭐106) - A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).

Libraries / Format Checking

• ChEMBL_Structure_Pipeline (formerly standardiser) (⭐173) - Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.

Libraries / Machine Learning

• ChemML (⭐148) - ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)

• chemmodlab (⭐12) - A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.

Libraries / Others

• OPSIN (⭐126) - Open Parser for Systematic IUPAC nomenclature

Resources / Courses

• Cheminformatics OLCC - Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of Arkansas at Little Rock by Robert Belford

Libraries / Molecular Descriptors

• DescriptaStorus (⭐201) - Descriptor computation(chemistry) and (optional) storage for machine learning.

Libraries / Docking

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

Libraries / General Purpose

• MolecularGraph.jl (⭐183) - A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia

Resources / Blogs

• Cheminformatics 2.0 - Blog of Alex M. Clark, a research scientist at Collaborative Drug Discovery.

• Depth-First - Blog of Richard L. Apodaca, a chemist living in La Jolla, California.

See Also / Books

• MolSSI Molecular Software Database ＊Pages created by Tobias Kind, PhD

Libraries / Web APIs

• CIRpy - Python wrapper for the NCI Chemical Identifier Resolver (CIR).

• chemminetools (⭐35) - Open source web framework for small molecule analysis based on Django.

Libraries / General Purpose

• ChemPy (⭐503) - A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)

Libraries / Others

• eiR (⭐3) - Accelerated similarity searching of small molecules

Libraries / Machine Learning

• OpenChem (⭐645) - OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.

Libraries / Molecular Dynamics

• NAMD - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Applications / Command Line Tools

• BCL::Commons

Libraries / Others

• Cookiecutter for Computational Molecular Sciences (⭐353) - Python-centric Cookiecutter for Molecular Computational Chemistry Packages by MolSSL

Resources / Courses

• Python for chemoinformatics (⭐217)

Resources / Courses

• Simulation in Chemistry and Biochemistry - by Dr. Jay Ponder, a professor from WashU St.Louis.

Resources / Courses

• Molecular modeling course - by Dr. Jay Ponder, a professor from WashU St.Louis.

Applications / Visualization

• 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.

Applications / Virtual Machine

• myChEMBL - A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)

Libraries / Visualization

• nglviewer - Interactive molecular graphics for Jupyter notebooks.

Applications / Virtual Machine

• 3D e-Chem Virtual Machine (⭐16) - Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows

Resources / Books

• Molecular Descriptors for Chemoinformatics - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.

Libraries / Molecular Descriptors

• Rcpi - R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.

Libraries / Format Checking

• rd_filters (⭐119) - A script to run structural alerts using the RDKit and ChEMBL

Libraries / Machine Learning

• DeepChem (⭐5k) - Deep learning library for Chemistry based on Tensorflow

• pytorch-geometric - A PyTorch library provides implementation of many graph convolution algorithms.

Applications / Visualization

• DataWarrior - A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.

Resources / Courses

• BigChem - All lectures of BigChem (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)

Libraries / Visualization

• 3Dmol.js (⭐741) - An object-oriented, webGL based JavaScript library for online molecular visualization.

Resources / Blogs

• Is life worth living? - Some examples for cheminformatics libraries.

Resources / Blogs

• DrugDiscovery.NET - Blog of Andreas Bender, who is a Reader for Molecular Informatics at University of Cambridge.

Resources / Courses

• TeachOpenCADD (⭐650) - A teaching platform for computer-aided drug design (CADD) using open source packages and data.

Applications / Command Line Tools

• Packmol - Initial configurations for molecular dynamics simulations by packing optimization.

Libraries / Machine Learning

• chainer-chemistry (⭐604) - A Library for Deep Learning in Biology and Chemistry.

Libraries / Molecular Descriptors

• Align-it - Align molecules according their pharmacophores.

Resources / Blogs

• Open Source Molecular Modeling - Updateable catalog of open source molecular modeling software.

• Noel O'Blog - Blog of Noel O'Boyle, who is a Senior Software Engineer at NextMove Software.

See Also / Books

• deeplearning-biology (⭐1.9k) - Chemoinformatics and drug discovery section in deeplearning-biology repo.

Libraries / Visualization

• rdeditor (⭐75) - Simple RDKit molecule editor GUI using PySide.

Journals / Others

• Journal of Cheminformatics

• Journal of Chemical Information and Modeling (ACS Publications)

Resources / Blogs

• Practical Cheminformatics - Blog with in-depth examples of practical application of cheminformatics.

Resources / Books

• Chemoinformatics for Drug Discovery - Materials about how to use Chemoinformatics strategies to improve drug discovery results.

Resources / Books

• Computational Approaches in Cheminformatics and Bioinformatics - Include insights from public (NIH), academic, and industrial sources at the same time.

Libraries / Databases

• razi (⭐37) - Cheminformatic extension for the SQLAlchemy database.

Libraries / General Purpose

• CDK (Chemistry Development Kit) - Algorithms for structural chemo- and bioinformatics, implemented in Java.

Libraries / Visualization

• JChemPaint (⭐106) - Chemical 2D structure editor application/applet based on the Chemistry Development Kit.

Applications / Command Line Tools

• MayaChemTools - Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs.

Libraries / Molecular Dynamics

• cclib (⭐301) - Parsers and algorithms for computational chemistry logfiles.

Applications / Visualization

• 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.

Applications / Command Line Tools

• Open Babel - Chemical toolbox designed to speak the many languages of chemical data.

Applications / Docking

• AutoDock Vina - Molecular docking and virtual screening.

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

Libraries / General Purpose

• RDKit - Collection of cheminformatics and machine-learning software written in C++ and Python.

• Indigo (⭐270) - 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.

• ChemmineR - Cheminformatics package for analyzing drug-like small molecule data in R.

Libraries / Format Checking

• MolVS (⭐143) - Molecule validation and standardization based on RDKit.

Libraries / Visualization

• Kekule.js - Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.

Libraries / Molecular Descriptors

• mordred (⭐317) - Molecular descriptor calculator based on RDKit.

• mol2vec (⭐239) - Vector representations of molecular substructures.

Libraries / Web APIs

• webchem (⭐153) - Chemical Information from the Web.

• Beaker (⭐47) - RDKit and OSRA in the Bottle on Tornado.

Libraries / 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 (⭐533) - Analysis of molecular dynamics trajectories.

Resources / Courses

• Learncheminformatics.com - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.

Resources / Blogs

• PubChem Blog - News, updates and tutorials about PubChem.

• The ChEMBL-og blog - Stories and news from Computational Chemical Biology Group at EMBL-EBI.

• ChEMBL blog - ChEMBL on GitHub.

• SteinBlog - Blog of Christoph Steinbeck, who is the head of cheminformatics and metabolism at the EMBL-EBI.

• chem-bla-ics - Blog of Egon Willighagen, who is an assistant professor at Maastricht University.

• steeveslab-blog - Some examples using RDKit.

Libraries / Web APIs

• PubChemPy - Python wrapper for the PubChem PUG REST API.

• ChemSpiPy - Python wrapper for the ChemSpider API.

Resources / Blogs

• So much to do, so little time - Trying to squeeze sense out of chemical data - Bolg of Rajarshi Guha, who is a research scientist at NIH Center for Advancing Translational Science.  * Some old blogs 1 2.

• Macs in Chemistry - Provide a resource for chemists using Apple Macintosh computers.

See Also / Books

• awesome-python-chemistry (⭐999) - Another list focuses on Python stuff related to Chemistry.