awesome-cheminformatics

Cheminformatics toolkit

A curated collection of Cheminformatics software and libraries for various tasks such as visualization, docking, and molecular analysis.

A curated list of Cheminformatics libraries and software.

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Awesome Cheminformatics / Applications / Visualization

PyMOLPython-enhanced molecular graphics tool
JmolBrowser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D
VMDMolecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
ChimeraHighly extensible program for interactive molecular visualization and analysis. is available
ChimeraXThe next-generation molecular visualization program, following UCSF Chimera. Source is available
DataWarriorA program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence

Awesome Cheminformatics / Applications / Command Line Tools

Open BabelChemical toolbox designed to speak the many languages of chemical data
MayaChemToolsCollection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs
PackmolInitial configurations for molecular dynamics simulations by packing optimization
BCL::Commons

Awesome Cheminformatics / Applications / Docking

AutoDock VinaMolecular docking and virtual screening
sminaCustomized to better support scoring function development and high-performance energy minimization

Awesome Cheminformatics / Applications / Virtual Machine

myChEMBLA version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)
3D e-Chem Virtual Machine16almost 8 years agoVirtual machine with all software and sample data to run 3D-e-Chem Knime workflows

Awesome Cheminformatics / Libraries / General Purpose

RDKitCollection of cheminformatics and machine-learning software written in C++ and Python
Indigo318almost 2 years agoUniversal 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
ChemmineRCheminformatics package for analyzing drug-like small molecule data in R
ChemPy560about 2 years agoA Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
MolecularGraph.jl202almost 2 years agoA graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
datamol476over 2 years ago: - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit
CGRtools43almost 4 years agoToolkit 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

Awesome Cheminformatics / Libraries / Format Checking

ChEMBL_Structure_Pipeline (formerly standardiser)197about 2 years agoTool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises
MolVS163over 6 years agoMolecule validation and standardization based on
rd_filters132about 3 years agoA script to run structural alerts using the RDKit and ChEMBL
pdb-tools391about 2 years agoA swiss army knife for manipulating and editing PDB files

Awesome Cheminformatics / Libraries / Visualization

Kekule.jsFront-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers
3Dmol.js825almost 2 years agoAn object-oriented, webGL based JavaScript library for online molecular visualization
JChemPaint115over 2 years agoChemical 2D structure editor application/applet based on the
rdeditor137about 2 years agoSimple RDKit molecule editor GUI using PySide
nglviewerInteractive molecular graphics for Jupyter notebooks
RDKit.jsOfficial JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics

Awesome Cheminformatics / Libraries / Molecular Descriptors

mordred376over 2 years agoMolecular descriptor calculator based on
DescriptaStorus237almost 2 years agoDescriptor computation(chemistry) and (optional) storage for machine learning
mol2vec258about 4 years agoVector representations of molecular substructures
Align-itAlign molecules according their pharmacophores
RcpiR/Bioconductor package to generate various descriptors of proteins, compounds and their interactions

Awesome Cheminformatics / Libraries / Machine Learning

DeepChem5,599almost 2 years agoDeep learning library for Chemistry based on Tensorflow
Chemprop1,827almost 2 years agoDirected message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation
ChemML163almost 3 years agoChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
olorenchemengine98about 3 years agoMolecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning
OpenChem684almost 3 years agoOpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend
DGL-LifeSci734almost 3 years agoDGL-LifeSci is a -based package for various applications in life science with graph neural network
chainer-chemistry641over 3 years agoA Library for Deep Learning in Biology and Chemistry
pytorch-geometricA PyTorch library provides implementation of many graph convolution algorithms
chemmodlab15over 3 years agoA Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R
Summit124about 2 years agoA python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks)

Awesome Cheminformatics / Libraries / Web APIs

webchem164over 2 years agoChemical Information from the Web
PubChemPyPython wrapper for the PubChem PUG REST API
ChemSpiPyPython wrapper for the ChemSpider API
CIRpyPython wrapper for the
Beaker49over 2 years agoand in the on
chemminetools36almost 4 years agoOpen source web framework for small molecule analysis based on Django
ambitoffers chemoinformatics functionality via REST web services

Awesome Cheminformatics / Libraries / Databases

razi38over 3 years agoCheminformatic extension for the SQLAlchemy database
Chemical Translation ServiceSource code of the web service

Awesome Cheminformatics / Libraries / Docking

RosettaA comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking
DOCKSTRING161almost 2 years agoAutomates and standardizes ligand preparation for AutoDock Vina

Awesome Cheminformatics / Libraries / Molecular Dynamics

GromacsMolecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids
OpenMMHigh performance toolkit for molecular simulation including extensive language bindings for Python, C, C++, and even Fortran
NAMDa parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
MDTraj602almost 2 years agoAnalysis of molecular dynamics trajectories
cclib339almost 2 years agoParsers and algorithms for computational chemistry logfiles
ProDy439almost 2 years agoA Python package for protein dynamics analysis

Awesome Cheminformatics / Libraries / Others

eiR3over 3 years agoAccelerated similarity searching of small molecules
OPSIN161almost 2 years agoOpen Parser for Systematic IUPAC nomenclature
Cookiecutter for Computational Molecular Sciences404about 2 years agoPython-centric Cookiecutter for Molecular Computational Chemistry Packages by
Auto-QChem88almost 2 years agoan automated workflow for the generation and storage of DFT calculations for organic molecules
Gypsum-DLa program for converting 2D SMILES strings to 3D models
RDchiral155about 3 years agoWrapper for RDKit's RunReactants to improve stereochemistry handling
confgen5almost 3 years agoWebapp for generating conformers

Awesome Cheminformatics / Journals

Journal of Cheminformatics
Journal of Chemical Information and Modeling (ACS Publications)

Awesome Cheminformatics / Resources / Courses

Learncheminformatics.com"Cheminformatics: Navigating the world of chemical data" courese at Indiana University
Python for chemoinformatics223about 5 years ago
TeachOpenCADD792about 2 years agoA teaching platform for computer-aided drug design (CADD) using open source packages and data
Cheminformatics OLCCCheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of Arkansas at Little Rock by Robert Belford
BigChemAll lectures of (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
Molecular modeling courseby Dr. , a professor from WashU St.Louis
Simulation in Chemistry and Biochemistryby Dr. , a professor from WashU St.Louis

Awesome Cheminformatics / Resources / Blogs

Open Source Molecular ModelingUpdateable catalog of open source molecular modeling software
PubChem BlogNews, updates and tutorials about
The ChEMBL-og blogStories and news from Computational Chemical Biology Group at
ChEMBL blogChEMBL on GitHub
SteinBlogBlog of , who is the head of cheminformatics and metabolism at the EMBL-EBI
Practical CheminformaticsBlog with in-depth examples of practical application of cheminformatics
So much to do, so little time - Trying to squeeze sense out of chemical dataBolg of , who is a research scientist at NIH Center for Advancing Translational Science.  * Some old blogs
Noel O'BlogBlog of , who is a Senior Software Engineer at NextMove Software
chem-bla-icsBlog of , who is an assistant professor at Maastricht University
steeveslab-blogSome examples using
Macs in ChemistryProvide a resource for chemists using Apple Macintosh computers
DrugDiscovery.NETBlog of , who is a Reader for Molecular Informatics at University of Cambridge
Is life worth living?Some examples for cheminformatics libraries
Cheminformatics 2.0Blog of , a research scientist at Collaborative Drug Discovery
Depth-FirstBlog of , a chemist living in La Jolla, California
CheminformaniaBlog of , who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca

Awesome Cheminformatics / Resources / Books

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

Awesome Cheminformatics / See Also

deeplearning-biology2,026about 2 years agoChemoinformatics and drug discovery section in deeplearning-biology repo
awesome-python-chemistry1,152almost 2 years agoAnother list focuses on Python stuff related to Chemistry
awesome-small-molecule-ml207almost 3 years agoA list of papers, data sets, and other resources for machine learning for small-molecule drug discovery
awesome-molecular-docking94over 3 years agoA curated list of molecular docking software, datasets, and other closely related resources
MolSSI Molecular Software Database＊

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