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 !
- 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.
- AutoDock Vina - Molecular docking and virtual screening.
- smina - Customized AutoDock Vina to better support scoring function development and high-performance energy minimization.
- myChEMBL - A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)
- 3D e-Chem Virtual Machine -
- 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
- 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
- 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.
- 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.
- 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.
- 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.
- razi - Cheminformatic extension for the SQLAlchemy database.
- Rosetta - A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.
- 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.
- 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
- 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.
- 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. <!---
- Asad's Blog - Bolg of Syed Asad Rahman, who is a research scientist in the Thornton group at EMBL-EBI. →
- 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.
- 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.
- deeplearning-biology - Chemoinformatics and drug discovery section in deeplearning-biology repo.
- awesome-python-chemistry - Another list focuses on Python stuff related to Chemistry.
- MolSSI Molecular Software Database ＊Pages created by Tobias Kind, PhD