awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

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Awesome Cheminformatics / 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. is available
ChimeraX The next-generation molecular visualization program, following UCSF Chimera. Source is available
DataWarrior A 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 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

Awesome Cheminformatics / Applications / Docking

AutoDock Vina Molecular docking and virtual screening
smina Customized to better support scoring function development and high-performance energy minimization

Awesome Cheminformatics / Applications / Virtual Machine

myChEMBL A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)
3D e-Chem Virtual Machine 16 about 6 years ago Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows

Awesome Cheminformatics / Libraries / General Purpose

RDKit Collection of cheminformatics and machine-learning software written in C++ and Python
Indigo 315 4 days ago 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 548 27 days ago A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
MolecularGraph.jl 198 17 days ago A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
datamol 459 4 months ago : - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit
CGRtools 43 almost 2 years ago 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

Awesome Cheminformatics / Libraries / Format Checking

ChEMBL_Structure_Pipeline (formerly standardiser) 186 about 1 month ago Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises
MolVS 154 over 4 years ago Molecule validation and standardization based on
rd_filters 126 about 1 year ago A script to run structural alerts using the RDKit and ChEMBL
pdb-tools 385 about 1 month ago A swiss army knife for manipulating and editing PDB files

Awesome Cheminformatics / Libraries / 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 794 about 1 month ago An object-oriented, webGL based JavaScript library for online molecular visualization
JChemPaint 113 4 months ago Chemical 2D structure editor application/applet based on the
rdeditor 132 25 days ago 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

Awesome Cheminformatics / Libraries / Molecular Descriptors

mordred 359 8 months ago Molecular descriptor calculator based on
DescriptaStorus 226 6 days ago Descriptor computation(chemistry) and (optional) storage for machine learning
mol2vec 251 about 2 years ago 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

Awesome Cheminformatics / Libraries / Machine Learning

DeepChem 5,427 5 days ago Deep learning library for Chemistry based on Tensorflow
Chemprop 1,725 8 days ago Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation
ChemML 162 about 1 year ago ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
olorenchemengine 97 about 1 year ago Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning
OpenChem 672 11 months ago OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend
DGL-LifeSci 716 12 months ago DGL-LifeSci is a -based package for various applications in life science with graph neural network
chainer-chemistry 629 over 1 year ago A Library for Deep Learning in Biology and Chemistry
pytorch-geometric A PyTorch library provides implementation of many graph convolution algorithms
chemmodlab 15 over 1 year ago A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R
Summit 120 about 1 month ago A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks)

Awesome Cheminformatics / Libraries / Web APIs

webchem 161 8 months ago 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
Beaker 48 6 months ago and in the on
chemminetools 36 almost 2 years ago Open source web framework for small molecule analysis based on Django
ambit offers chemoinformatics functionality via REST web services

Awesome Cheminformatics / Libraries / Databases

razi 38 over 1 year ago Cheminformatic extension for the SQLAlchemy database
Chemical Translation Service Source code of the web service

Awesome Cheminformatics / Libraries / Docking

Rosetta A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking
DOCKSTRING 155 2 months ago Automates and standardizes ligand preparation for AutoDock Vina

Awesome Cheminformatics / 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
NAMD a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
MDTraj 586 1 day ago Analysis of molecular dynamics trajectories
cclib 330 5 days ago Parsers and algorithms for computational chemistry logfiles
ProDy 427 10 days ago A Python package for protein dynamics analysis

Awesome Cheminformatics / Libraries / Others

eiR 3 over 1 year ago Accelerated similarity searching of small molecules
OPSIN 147 20 days ago Open Parser for Systematic IUPAC nomenclature
Cookiecutter for Computational Molecular Sciences 385 about 1 month ago Python-centric Cookiecutter for Molecular Computational Chemistry Packages by
Auto-QChem 85 1 day ago 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 154 about 1 year ago Wrapper for RDKit's RunReactants to improve stereochemistry handling
confgen 5 11 months ago Webapp 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 chemoinformatics 222 over 3 years ago
TeachOpenCADD 761 3 months ago 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 (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
Molecular modeling course by Dr. , a professor from WashU St.Louis
Simulation in Chemistry and Biochemistry by Dr. , a professor from WashU St.Louis

Awesome Cheminformatics / Resources / Blogs

Open Source Molecular Modeling Updateable catalog of open source molecular modeling software
PubChem Blog News, updates and tutorials about
The ChEMBL-og blog Stories and news from Computational Chemical Biology Group at
ChEMBL blog ChEMBL on GitHub
SteinBlog Blog of , 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 , who is a research scientist at NIH Center for Advancing Translational Science.  * Some old blogs
Noel O'Blog Blog of , who is a Senior Software Engineer at NextMove Software
chem-bla-ics Blog of , who is an assistant professor at Maastricht University

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