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 !

Contents

• Applications
  • Visualization
  • Command Line Tools
  • Docking
  • Virtual Machine
• Libraries
  • General Purpose
  • Visualization
  • Command Line Tools
  • Docking
  • Molecular Descriptors
  • Machine Learning
  • Web APIs
  • Databases
  • Others
• 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
• 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.

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

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

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.

See Also

• deeplearning-biology - Chemoinformatics and drug discovery section in deeplearning-biology repo.
• awesome-python-chemistry - Another list focuses on Python stuff related to Chemistry.
• awesome-small-molecule-ml - A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.
• awesome-molecular-docking - A curated list of molecular docking software, datasets, and other closely related resources.
• MolSSI Molecular Software Database ＊Pages created by Tobias Kind, PhD

License