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Awesome Cheminformatics

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 !

Applications
Libraries
Journals
Resources
- Courses
- Blogs
- Books
See Also

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.
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

Docking

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

Libraries

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

ChEMBL_Structure_Pipeline (formerly 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
pdb-tools - A swiss army knife for manipulating and editing PDB files.

Visualization

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

webchem - Chemical Information from the Web.
PubChemPy - Python wrapper for the PubChem PUG REST API.
ChemSpiPy - Python wrapper for the ChemSpider API.
CIRpy - Python wrapper for the NCI Chemical Identifier Resolver (CIR).
Beaker - RDKit and OSRA in the Bottle on Tornado.
chemminetools - Open source web framework for small molecule analysis based on Django.
ambit - offers chemoinformatics functionality via REST web services.

Databases

razi - Cheminformatic extension for the SQLAlchemy database.
Chemical Translation Service - Source code of the Chemical Translation Service web service.

Docking

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

Others

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

Journals

Resources

Courses

Learncheminformatics.com - “Cheminformatics: Navigating the world of chemical data” courese at Indiana University.
Python for chemoinformatics
TeachOpenCADD - A teaching platform for computer-aided drug design (CADD) using open source packages and data.
Cheminformatics OLCC - Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of Arkansas at Little Rock by Robert Belford
BigChem - All lectures of BigChem (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
Molecular modeling course - by Dr. Jay Ponder, a professor from WashU St.Louis.
Simulation in Chemistry and Biochemistry - by Dr. Jay Ponder, a professor from WashU St.Louis.

Blogs

Open Source Molecular Modeling - Updateable catalog of open source molecular modeling software.
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.
Practical Cheminformatics - Blog with in-depth examples of practical application of cheminformatics.
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.
Noel O’Blog - Blog of Noel O’Boyle, who is a Senior Software Engineer at NextMove Software.
chem-bla-ics - Blog of Egon Willighagen, who is an assistant professor at Maastricht University. <!—
Asad’s Blog - Bolg of Syed Asad Rahman, who is a research scientist in the Thornton group at EMBL-EBI. –>
steeveslab-blog - Some examples using RDKit.
Macs in Chemistry - Provide a resource for chemists using Apple Macintosh computers.
DrugDiscovery.NET - Blog of Andreas Bender, who is a Reader for Molecular Informatics at University of Cambridge.
Is life worth living? - Some examples for cheminformatics libraries.
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.
Cheminformania - Blog of Ph.D, Esben Jannik Bjerrum, who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.

Books

Computational Approaches in Cheminformatics and Bioinformatics - Include insights from public (NIH), academic, and industrial sources at the same time.
Chemoinformatics for Drug Discovery - Materials about how to use Chemoinformatics strategies to improve drug discovery results.
Molecular Descriptors for Chemoinformatics - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.