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An open API service indexing awesome lists of open source software.

awesome-cheminformatics

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

Last synced: 2 days ago
JSON representation

  • 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.
      • MolecularGraph.jl - A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
      • ChemPy - A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
      • 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.
      • 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.
      • 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.
      • 3Dmol.js - An object-oriented, webGL based JavaScript library for online molecular visualization.
      • Kekule.js - Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
      • JChemPaint - Chemical 2D structure editor application/applet based on the [Chemistry Development Kit](https://sourceforge.net/projects/cdk/).
      • rdeditor - Simple RDKit molecule editor GUI using PySide.
      • nglviewer - Interactive molecular graphics for Jupyter notebooks.
      • Kekule.js - Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.

    • Molecular Descriptors

      • Rcpi - R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.
      • mordred - Molecular descriptor calculator based on [RDKit](http://www.rdkit.org/).
      • DescriptaStorus - Descriptor computation(chemistry) and (optional) storage for machine learning.
      • mol2vec - Vector representations of molecular substructures.

    • Machine Learning

      • pytorch-geometric - A PyTorch library provides implementation of many graph convolution algorithms.
      • DeepChem - Deep learning library for Chemistry based on Tensorflow
      • Summit - A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).
      • DGL-LifeSci - DGL-LifeSci is a [DGL](https://www.dgl.ai/)-based package for various applications in life science with graph neural network.
      • OpenChem - OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.
      • Chemprop - Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
      • ChemML - ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
      • chemmodlab - A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.
      • olorenchemengine - Molecular property prediction with unified API for diverse models and respresentations,

    • 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.
      • ambit - offers chemoinformatics functionality via REST web services.
      • webchem - Chemical Information from the Web.
      • chemminetools - Open source web framework for small molecule analysis based on Django.
      • 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/).

    • Databases

      • Chemical Translation Service - Source code of the [Chemical Translation Service](https://cts.fiehnlab.ucdavis.edu/) web service.
      • razi - Cheminformatic extension for the SQLAlchemy database.

    • Docking

      • Rosetta - A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.
      • DOCKSTRING - Automates and standardizes ligand preparation for AutoDock Vina.
      • 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.
      • cclib - Parsers and algorithms for computational chemistry logfiles.
      • MDTraj - Analysis of molecular dynamics trajectories.
      • ProDy - A Python package for protein dynamics analysis
      • 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.
      • 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](https://molssi.org/)
      • Auto-QChem - an automated workflow for the generation and storage of DFT calculations for organic molecules.
      • RDchiral - Wrapper for RDKit's RunReactants to improve stereochemistry handling
      • confgen - Webapp for generating conformers

    • 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.
      • rd_filters - A script to run structural alerts using the RDKit and ChEMBL
      • pdb-tools - A swiss army knife for manipulating and editing PDB files.
      • MolVS - Molecule validation and standardization based on [RDKit](http://www.rdkit.org/).

  • 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.
      • VMD - Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
      • Jmol - Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D.

    • Command Line Tools

      • MayaChemTools - Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs.
      • MayaChemTools - Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs.
      • Open Babel - Chemical toolbox designed to speak the many languages of chemical data.

    • 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)
      • 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

  • Journals

  • Resources

  • See Also

Programming Languages
Python 14 Jupyter Notebook 4 Java 1 C++ 1 R 1 Julia 1
Categories
Libraries 61 Resources 31 Applications 17 See Also 7 Journals 2 License 1
Sub Categories
Blogs 23 Visualization 16 Books 11 Machine Learning 9 Others 9 Molecular Dynamics 8 General Purpose 8 Web APIs 8 Docking 6 Courses 5 Format Checking 4 Molecular Descriptors 4 Command Line Tools 3 Virtual Machine 3 Databases 2
Keywords
drug-discovery 8 chemistry 6 machine-learning 5 python 5 cheminformatics 5 computational-chemistry 4 deep-learning 4 bioinformatics 3 quantum-chemistry 3 molecular-modeling 2 computational-biology 2 molecule 2 neural-networks 2 cas-number 1 chemical-information 1 chemspider 1 awesome-list 1 identifier 1 r 1 r-package 1 ropensci 1 rstats 1 webscraping 1 bayesian-optimization 1 nelder-mead 1 awesome 1 scikit-learn 1 rdkit 1 jupyter 1 chemoinformatics 1 toolkit 1 mcs 1 julia-language 1 julia 1 graph 1 materials-science 1 biology 1 simulation 1 python-chemistry 1 molecular-dynamics 1 pdb 1 protein 1 rcsb 1 structural-bioinformatics 1 structural-biology 1 utrecht-university 1 data-science 1 materials-informatics 1 quantum-mechanics 1 bingo 1