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.