Cheminformatics

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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

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.

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.

Cheminformatics

Awesome Cheminformatics

Applications

Visualization

Command Line Tools

Docking

Virtual Machine

Libraries

General Purpose

Format Checking

Visualization

Molecular Descriptors

Machine Learning

Web APIs

Databases

Docking

Molecular Dynamics

Others

Journals

Resources

Courses

Blogs

Books

See Also