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awesome-cheminformatics

A curated list of Cheminformatics libraries and software.
https://github.com/hsiaoyi0504/awesome-cheminformatics

Last synced: 4 days ago
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  • 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](https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html) is available.
      • 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 - A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.
      • Jmol - Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D.
      • 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](http://vina.scripps.edu/) to better support scoring function development and high-performance energy minimization.
      • AutoDock Vina - Molecular docking and virtual screening.

    • Virtual Machine

      • myChEMBL - A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)

  • Libraries

    • General Purpose

      • RDKit - Collection of cheminformatics and machine-learning software written in C++ and Python.
      • 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.
      • datamol - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.

    • Visualization

      • 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

      • Align-it - Align molecules according their pharmacophores.
      • Rcpi - R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.

    • Machine Learning

      • pytorch-geometric - A PyTorch library provides implementation of many graph convolution algorithms.
      • chainer-chemistry - A Library for Deep Learning in Biology and Chemistry.

    • Web APIs

      • 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)](https://cactus.nci.nih.gov/chemical/structure).
      • ambit - offers chemoinformatics functionality via REST web services.
      • 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)](https://cactus.nci.nih.gov/chemical/structure).
      • ambit - offers chemoinformatics functionality via REST web services.
      • ambit - offers chemoinformatics functionality via REST web services.

    • Databases

    • 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.
      • 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.

    • Others

      • Gypsum-DL - a program for converting 2D SMILES strings to 3D models.
      • Auto-QChem - an automated workflow for the generation and storage of DFT calculations for organic molecules.

  • Journals

  • Resources

    • Courses

      • Learncheminformatics.com - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.
      • 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](http://bigchem.eu/) (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
      • Molecular modeling course - by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis.
      • Simulation in Chemistry and Biochemistry - by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis.
      • Learncheminformatics.com - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.

    • Blogs

      • Open Source Molecular Modeling - Updateable catalog of open source molecular modeling software.
      • PubChem Blog - News, updates and tutorials about [PubChem](https://pubchem.ncbi.nlm.nih.gov/).
      • The ChEMBL-og blog - Stories and news from Computational Chemical Biology Group at [EMBL-EBI](https://www.ebi.ac.uk/).
      • ChEMBL blog - ChEMBL on GitHub.
      • 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 - 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](http://blog.rguha.net/?page_id=8), who is a research scientist at NIH Center for Advancing Translational Science.
      • 1
      • Noel O'Blog - Blog of [Noel O'Boyle](https://www.redbrick.dcu.ie/~noel/), who is a Senior Software Engineer at NextMove Software.
      • chem-bla-ics - Blog of [Egon Willighagen](http://egonw.github.io/), 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](http://www.ebi.ac.uk/research/thornton) at EMBL-EBI.
      • steeveslab-blog - Some examples using [RDKit](http://www.rdkit.org/).
      • Macs in Chemistry - Provide a resource for chemists using Apple Macintosh computers.
      • 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? - Some examples for cheminformatics libraries.
      • Cheminformatics 2.0 - Blog of [Alex M. Clark](https://twitter.com/aclarkxyz), a research scientist at Collaborative Drug Discovery.
      • Depth-First - Blog of [Richard L. Apodaca](https://depth-first.com/about/), a chemist living in La Jolla, California.
      • Cheminformania - Blog of [Ph.D, Esben Jannik Bjerrum](https://www.cheminformania.com/about/esben-jannik-bjerrum/), who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.
      • PubChem Blog - News, updates and tutorials about [PubChem](https://pubchem.ncbi.nlm.nih.gov/).
      • The ChEMBL-og blog - Stories and news from Computational Chemical Biology Group at [EMBL-EBI](https://www.ebi.ac.uk/).
      • Noel O'Blog - Blog of [Noel O'Boyle](https://www.redbrick.dcu.ie/~noel/), who is a Senior Software Engineer at NextMove Software.
      • chem-bla-ics - Blog of [Egon Willighagen](http://egonw.github.io/), who is an assistant professor at Maastricht University.
      • Macs in Chemistry - Provide a resource for chemists using Apple Macintosh computers.
      • Cheminformania - Blog of [Ph.D, Esben Jannik Bjerrum](https://www.cheminformania.com/about/esben-jannik-bjerrum/), who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.

    • Books

  • See Also

Categories
Resources 34 Libraries 28 Applications 16 License 4 See Also 3 Journals 2
Sub Categories
Blogs 24 Books 11 Visualization 10 Web APIs 9 Courses 6 Molecular Dynamics 5 Command Line Tools 4 General Purpose 4 Docking 4 Others 4 Machine Learning 2 Molecular Descriptors 2 Virtual Machine 1 Databases 1