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# Cheminformatics

**repo:** [hsiaoyi0504/awesome-cheminformatics](https://github.com/hsiaoyi0504/awesome-cheminformatics)  
**category:** [[miscellaneous|Miscellaneous]]

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# Awesome Cheminformatics [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)

> 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](https://en.wikipedia.org/wiki/Cheminformatics)

A curated list of awesome Cheminformatics software, resources, and libraries. Mostly command line based, and free or open-source. Please feel free to [contribute](CONTRIBUTING.md) !

## Contents

* [Applications](#applications)
  * [Visualization](#app-visualization)
  * [Command Line Tools](#app-cmd)
  * [Docking](#app-docking)
  * [Virtual Machine](#app-virtual)
* [Libraries](#libraries)
  * [General Purpose](#lib-general)
  * [Visualization](#lib-visualization)
  * [Command Line Tools](#lib-format)
  * [Docking](#lib-dock)
  * [Molecular Descriptors](#lib-des)
  * [Machine Learning](#lib-ml)
  * [Web APIs](#lib-web)
  * [Databases](#lib-db)
  * [Others](#lib-others)
* [Journals](#journals)
* [Resources](#resources)
  * [Courses](#courses)
  * [Blogs](#blogs)
  * [Books](#books)
* [See Also](#see-also)

## Applications

<a id="app-visualization"></a>
### Visualization

* [PyMOL](https://sourceforge.net/projects/pymol/) - [Python](/@harrisonqian/awesome/wiki/programming-languages/python)-enhanced molecular graphics tool.
* [Jmol](http://jmol.sourceforge.net/) - Browser-based [HTML5](/@harrisonqian/awesome/wiki/front-end-development/html5) viewer and stand-alone [Java](/@harrisonqian/awesome/wiki/programming-languages/java) viewer for chemical structures in 3D.
* [VMD](http://www.ks.uiuc.edu/Research/vmd/) - Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
* [Chimera](https://www.cgl.ucsf.edu/chimera/) - Highly extensible program for interactive molecular visualization and analysis. [Source](https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html) is available.
* [ChimeraX](https://www.cgl.ucsf.edu/chimerax/) - The next-generation molecular visualization program, following UCSF Chimera. Source is available [here](https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html).
* [DataWarrior](http://www.openmolecules.org/datawarrior/index.html) - A program for [data Visualization](/@harrisonqian/awesome/wiki/miscellaneous/data-visualization) and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.

<a id="app-cmd"></a>
### Command Line Tools

* [Open Babel](http://openbabel.org/wiki/Main_Page) - Chemical toolbox designed to speak the many languages of chemical data.
* [MayaChemTools](http://www.mayachemtools.org/index.html) - Collection of [Perl](/@harrisonqian/awesome/wiki/programming-languages/perl) and [Python](/@harrisonqian/awesome/wiki/programming-languages/python) scripts, modules, and classes that support day-to-day computational discovery needs.
* [Packmol](http://m3g.iqm.unicamp.br/packmol/home.shtml) - Initial configurations for molecular dynamics simulations by packing optimization.
* [BCL::Commons](http://meilerlab.org/index.php/bclcommons/show/b_apps_id/1)

<a id="app-docking"></a>
### Docking

* [AutoDock Vina](http://vina.scripps.edu/) - Molecular docking and virtual screening.
* [smina](https://sourceforge.net/projects/smina/) - Customized [AutoDock Vina](http://vina.scripps.edu/) to better support scoring function development and high-performance energy minimization.

<a id="app-virtual"></a>
### Virtual Machine

* [myChEMBL](http://chembl.blogspot.com/2015/07/mychembl-20-has-landed.html) - A version of ChEMBL built using Open Source software (Ubuntu, [PostgreSQL](/@harrisonqian/awesome/wiki/databases/postgresql), RDKit)
* [3D e-Chem Virtual Machine](https://github.com/3D-e-Chem/3D-e-Chem-VM) - Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows

## Libraries

<a id="lib-general"></a>
### General Purpose

* [RDKit](http://www.rdkit.org/) - Collection of cheminformatics and machine-[learning](/@harrisonqian/awesome/wiki/programming-languages/learning) software written in C++ and [Python](/@harrisonqian/awesome/wiki/programming-languages/python).
* [Indigo](https://github.com/epam/Indigo) - Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with [Java](/@harrisonqian/awesome/wiki/programming-languages/java), C#, and [Python](/@harrisonqian/awesome/wiki/programming-languages/python) wrappers.
* [CDK (Chemistry Development Kit)](https://sourceforge.net/projects/cdk/) - [Algorithms](/@harrisonqian/awesome/wiki/theory/algorithms) for structural chemo- and [bioinformatics](/@harrisonqian/awesome/wiki/miscellaneous/bioinformatics), implemented in [Java](/@harrisonqian/awesome/wiki/programming-languages/java).
* [ChemmineR](https://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html) - Cheminformatics package for analyzing drug-like small molecule data in R.
* [ChemPy](https://github.com/bjodah/chempy) - A [Python](/@harrisonqian/awesome/wiki/programming-languages/python) package useful for chemistry (mainly physical/inorganic/analytical chemistry)
* [MolecularGraph.jl](https://github.com/mojaie/MolecularGraph.jl) - A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in [Julia](/@harrisonqian/awesome/wiki/programming-languages/julia)
* [datamol](https://github.com/datamol-org/datamol): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
* [CGRtools](https://github.com/cimm-kzn/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.

<a id="lib-format"></a>
### Format Checking

* [ChEMBL_Structure_Pipeline (formerly standardiser)](https://github.com/chembl/ChEMBL_Structure_Pipeline) - Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.
* [MolVS](https://github.com/mcs07/MolVS) - Molecule validation and standardization based on [RDKit](http://www.rdkit.org/).
* [rd_filters](https://github.com/PatWalters/rd_filters) - A script to run structural alerts using the RDKit and ChEMBL
* [pdb-tools](https://github.com/haddocking/pdb-tools) - A swiss army knife for manipulating and editing PDB files.

<a id="lib-visualization"></a>
### Visualization

* [Kekule.js](http://partridgejiang.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/Kekule.js/) - Front-end [JavaScript](/@harrisonqian/awesome/wiki/programming-languages/javascript) library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
* [3Dmol.js](https://github.com/3dmol/3Dmol.js) - An object-oriented, [webGL](/@harrisonqian/awesome/wiki/front-end-development/webgl) based [JavaScript](/@harrisonqian/awesome/wiki/programming-languages/javascript) library for online molecular visualization.
* [JChemPaint](https://github.com/JChemPaint/jchempaint) - Chemical 2D structure editor application/applet based on the [Chemistry Development Kit](https://sourceforge.net/projects/cdk/).
* [rdeditor](https://github.com/EBjerrum/rdeditor) - Simple RDKit molecule editor GUI using PySide.
* [nglviewer](http://nglviewer.org/nglview/latest/) - Interactive molecular graphics for [Jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebooks.
* [RDKit.js](https://www.npmjs.com/package/@rdkit/rdkit) - Official [JavaScript](/@harrisonqian/awesome/wiki/programming-languages/javascript) distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.

<a id="lib-des"></a>
### Molecular Descriptors

* [mordred](https://github.com/mordred-descriptor/mordred) - Molecular descriptor calculator based on [RDKit](http://www.rdkit.org/).
* [DescriptaStorus](https://github.com/bp-kelley/descriptastorus) - Descriptor computation(chemistry) and (optional) storage for [machine learning](/@harrisonqian/awesome/wiki/computer-science/machine-learning).
* [mol2vec](https://github.com/samoturk/mol2vec) - Vector representations of molecular substructures.
* [Align-it](http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html#alignit-generating-pharmacophore-points) - Align molecules according their pharmacophores.
* [Rcpi](https://nanx.me/Rcpi/index.html) - R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.

<a id="lib-ml"></a>
### Machine Learning

* [DeepChem](https://github.com/deepchem/deepchem) - [Deep learning](/@harrisonqian/awesome/wiki/computer-science/deep-learning) library for Chemistry based on [Tensorflow](/@harrisonqian/awesome/wiki/computer-science/tensorflow)
* [Chemprop](https://github.com/chemprop/chemprop) - Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
* [ChemML](https://github.com/hachmannlab/chemml) - ChemML is a [machine learning](/@harrisonqian/awesome/wiki/computer-science/machine-learning) and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
* [olorenchemengine](https://github.com/Oloren-AI/olorenchemengine) - Molecular property prediction with unified API for diverse models and respresentations,
  with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.
* [OpenChem](https://github.com/Mariewelt/OpenChem) - OpenChem is a [deep learning](/@harrisonqian/awesome/wiki/computer-science/deep-learning) toolkit for Computational Chemistry with PyTorch backend.
* [DGL-LifeSci](https://github.com/awslabs/dgl-lifesci) - DGL-LifeSci is a [DGL](https://www.dgl.ai/)-based package for various applications in life science with graph neural network.
* [chainer-chemistry](https://github.com/pfnet-research/chainer-chemistry) - A Library for [Deep Learning](/@harrisonqian/awesome/wiki/computer-science/deep-learning) in Biology and Chemistry.
* [pytorch-geometric](https://pytorch-geometric.readthedocs.io/en/latest/) - A PyTorch library provides implementation of many graph convolution [algorithms](/@harrisonqian/awesome/wiki/theory/algorithms).
* [chemmodlab](https://github.com/jrash/ChemModLab) - A Cheminformatics Modeling Laboratory for Fitting and Assessing [Machine Learning](/@harrisonqian/awesome/wiki/computer-science/machine-learning) Models in R.
* [Summit](https://github.com/sustainable-processes/summit) - A [python](/@harrisonqian/awesome/wiki/programming-languages/python) package for optimizing chemical reactions using [machine learning](/@harrisonqian/awesome/wiki/computer-science/machine-learning) (contains 10 [algorithms](/@harrisonqian/awesome/wiki/theory/algorithms) + several benchmarks).

<a id="lib-web"></a>
### Web APIs

* [webchem](https://github.com/ropensci/webchem) - Chemical Information from the Web.
* [PubChemPy](http://pubchempy.readthedocs.io) - [Python](/@harrisonqian/awesome/wiki/programming-languages/python) wrapper for the PubChem PUG [REST](/@harrisonqian/awesome/wiki/miscellaneous/rest) API.
* [ChemSpiPy](http://chemspipy.readthedocs.org) - [Python](/@harrisonqian/awesome/wiki/programming-languages/python) wrapper for the ChemSpider API.
* [CIRpy](http://cirpy.readthedocs.org/) - [Python](/@harrisonqian/awesome/wiki/programming-languages/python) wrapper for the [NCI Chemical Identifier Resolver (CIR)](https://cactus.nci.nih.gov/chemical/structure).
* [Beaker](https://github.com/chembl/chembl_beaker) - [RDKit](http://www.rdkit.org/) and [OSRA](https://cactus.nci.nih.gov/osra/) in the [Bottle](http://bottlepy.org/docs/dev/) on [Tornado](http://www.tornadoweb.org/en/stable/).
* [chemminetools](https://github.com/girke-lab/chemminetools) - Open source web framework for small molecule analysis based on Django.
* [ambit](http://ambit.sourceforge.net/) - offers chemoinformatics functionality via [REST](/@harrisonqian/awesome/wiki/miscellaneous/rest) web services.

<a id="lib-db"></a>
### Databases

* [razi](https://github.com/rvianello/razi) - Cheminformatic extension for the [SQLAlchemy](/@harrisonqian/awesome/wiki/databases/sqlalchemy) [database](/@harrisonqian/awesome/wiki/databases/database).
* [Chemical Translation Service](https://bitbucket.org/fiehnlab/fiehnlab-cts/src/master/) - Source code of the [Chemical Translation Service](https://cts.fiehnlab.ucdavis.edu/) web service.

<a id="lib-dock"></a>
### Docking
* [Rosetta](https://www.rosettacommons.org/docs/latest/Home) - A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.
* [DOCKSTRING](https://github.com/dockstring/dockstring) - Automates and standardizes ligand preparation for AutoDock Vina.

<a id="lib-md"></a>
### Molecular Dynamics

* [Gromacs](http://www.gromacs.org/) - Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
* [OpenMM](http://openmm.org/) - High performance toolkit for molecular simulation including extensive language bindings for [Python](/@harrisonqian/awesome/wiki/programming-languages/python), C, C++, and even [Fortran](/@harrisonqian/awesome/wiki/programming-languages/fortran).
* [NAMD](https://www.ks.uiuc.edu/Research/namd/) - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
* [MDTraj](https://github.com/mdtraj/mdtraj) - Analysis of molecular dynamics trajectories.
* [cclib](https://github.com/cclib/cclib) - Parsers and [algorithms](/@harrisonqian/awesome/wiki/theory/algorithms) for computational chemistry logfiles.
* [ProDy](https://github.com/prody/ProDy) - A [Python](/@harrisonqian/awesome/wiki/programming-languages/python) package for protein dynamics analysis

<a id="lib-others"></a>
### Others

* [eiR](https://github.com/girke-lab/eiR) - Accelerated similarity searching of small molecules
* [OPSIN](https://github.com/dan2097/opsin) - Open Parser for Systematic IUPAC nomenclature
* [Cookiecutter for Computational Molecular Sciences](https://github.com/MolSSI/cookiecutter-cms) - [Python](/@harrisonqian/awesome/wiki/programming-languages/python)-centric Cookiecutter for Molecular Computational Chemistry Packages by [MolSSL](https://molssi.org/)
* [Auto-QChem](https://github.com/PrincetonUniversity/auto-qchem) - an automated workflow for the generation and storage of DFT calculations for organic molecules.
* [Gypsum-DL](https://git.durrantlab.pitt.edu/jdurrant/gypsum_dl) - a program for converting 2D SMILES strings to 3D models.
* [RDchiral](https://github.com/connorcoley/rdchiral) - Wrapper for RDKit's RunReactants to improve stereochemistry handling
* [confgen](https://github.com/Et9797/confgen-webapp) - Webapp for generating conformers
 
 
## Journals

* [Journal of Cheminformatics](https://jcheminf.biomedcentral.com/)
* [Journal of Chemical Information and Modeling (ACS Publications)](https://pubs.acs.org/journal/jcisd8)

## Resources

### Courses

* [Learncheminformatics.com](http://learncheminformatics.com/) - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.
* [Python for chemoinformatics](https://github.com/Mishima-syk/py4chemoinformatics)
* [TeachOpenCADD](https://github.com/volkamerlab/TeachOpenCADD) - A teaching platform for computer-aided drug design (CADD) using open source packages and data.
* [Cheminformatics OLCC](https://chem.libretexts.org/Courses/Intercollegiate_Courses/Cheminformatics_OLCC_(2019)) - Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of Arkansas at Little Rock by Robert Belford
* [BigChem](http://bigchem.eu/alllectures) - All lectures of [BigChem](http://bigchem.eu/) (A Horizon 2020 MSC ITN EID project, which provides innovative [education](/@harrisonqian/awesome/wiki/back-end-development/education) in large chemical data analysis.)
* [Molecular modeling course](https://dasher.wustl.edu/chem478/) - by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis.
* [Simulation in Chemistry and Biochemistry](https://dasher.wustl.edu/chem430/) - by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis.

### Blogs

* [Open Source Molecular Modeling](https://opensourcemolecularmodeling.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/README.html) - Updateable catalog of open source molecular modeling software.
* [PubChem Blog](https://pubchemblog.ncbi.nlm.nih.gov/) - News, updates and [tutorials](/@harrisonqian/awesome/wiki/computer-science/tutorials) about [PubChem](https://pubchem.ncbi.nlm.nih.gov/).
* [The ChEMBL-og blog](http://chembl.blogspot.tw/) - Stories and news from Computational Chemical Biology Group at [EMBL-EBI](https://www.ebi.ac.uk/).
* [ChEMBL blog](http://chembl.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/) - ChEMBL on [GitHub](/@harrisonqian/awesome/wiki/development-environment/github).
* [SteinBlog](http://www.steinbeck-molecular.de/steinblog/) - Blog of [Christoph Steinbeck](http://www.steinbeck-molecular.de/steinblog/index.php/about/), who is the head of cheminformatics and metabolism at the EMBL-EBI.
* [Practical Cheminformatics](http://practicalcheminformatics.blogspot.com/) - 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](http://blog.rguha.net/) - Bolg of [Rajarshi Guha](http://blog.rguha.net/?page_id=8), who is a research scientist at NIH Center for Advancing Translational Science.
  * Some old blogs [1](https://rguha.wordpress.com/) [2](http://www.rguha.net/index.html).
* [Noel O'Blog](http://baoilleach.blogspot.tw/) - Blog of [Noel O'Boyle](https://www.redbrick.dcu.ie/~noel/), who is a Senior Software Engineer at NextMove Software.
* [chem-bla-ics](http://chem-bla-ics.blogspot.tw/) - Blog of [Egon Willighagen](http://egonw.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/), who is an assistant professor at Maastricht University.

* [steeveslab-blog](http://asteeves.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/) - Some examples using [RDKit](http://www.rdkit.org/).
* [Macs in Chemistry](http://www.macinchem.org/) - Provide a resource for chemists using Apple Macintosh computers.
* [DrugDiscovery.NET](http://www.drugdiscovery.net/) - Blog of [Andreas Bender](http://www.andreasbender.de/), who is a Reader for Molecular Informatics at University of Cambridge.
* [Is life worth living?](https://iwatobipen.wordpress.com/) - Some examples for cheminformatics libraries.
* [Cheminformatics 2.0](https://cheminf20.org/) - Blog of [Alex M. Clark](https://twitter.com/aclarkxyz), a research scientist at Collaborative Drug Discovery.
* [Depth-First](https://depth-first.com/) - Blog of [Richard L. Apodaca](https://depth-first.com/about/), a chemist living in La Jolla, California.
* [Cheminformania](https://www.cheminformania.com) - Blog of [Ph.D, Esben Jannik Bjerrum](https://www.cheminformania.com/about/esben-jannik-bjerrum/), who is a Principle Scientist and a [Machine Learning](/@harrisonqian/awesome/wiki/computer-science/machine-learning) and AI specialists at AstraZeneca.

### Books

* [Computational Approaches in Cheminformatics and Bioinformatics](https://books.google.com/books/about/Computational_Approaches_in_Cheminformat.html?id=bLqV4rYQoYsC) -  Include insights from public (NIH), academic, and industrial sources at the same time.
* [Chemoinformatics for Drug Discovery](https://onlinelibrary.wiley.com/doi/book/10.1002/9781118742785) - Materials about how to use Chemoinformatics strategies to improve drug discovery results.
* [Molecular Descriptors for Chemoinformatics](https://onlinelibrary.wiley.com/doi/book/10.1002/9783527628766) - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.