Awesome Cheminformatics – Massive Collection of Resources

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.

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

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 –

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

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

Visulization

• 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.

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)
• OpenChem – OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.
• 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.

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.

Databases

• razi – Cheminformatic extension for the SQLAlchemy database.

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.

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

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.

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.