{"slug": "hsiaoyi0504--awesome-cheminformatics", "title": "Cheminformatics", "description": "A curated list of Cheminformatics libraries and software.", "github_url": "https://github.com/hsiaoyi0504/awesome-cheminformatics", "stars": "625", "tag": "Miscellaneous", "entry_count": 110, "subcategory_count": 18, "subcategories": [{"name": "General", "parent": "", "entries": [{"name": "Applications", "url": "#applications", "description": ""}, {"name": "Libraries", "url": "#libraries", "description": ""}, {"name": "Journals", "url": "#journals", "description": ""}, {"name": "Resources", "url": "#resources", "description": ""}, {"name": "See Also", "url": "#see-also", "description": ""}]}, {"name": "Visualization", "parent": "Applications", "entries": [{"name": "PyMOL", "url": "https://sourceforge.net/projects/pymol/", "description": "Python-enhanced molecular graphics tool."}, {"name": "Jmol", "url": "http://jmol.sourceforge.net/", "description": "Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D."}, {"name": "VMD", "url": "http://www.ks.uiuc.edu/Research/vmd/", "description": "Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting."}, {"name": "Chimera", "url": "https://www.cgl.ucsf.edu/chimera/", "description": "Highly extensible program for interactive molecular visualization and analysis. [Source](https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html) is available."}, {"name": "ChimeraX", "url": "https://www.cgl.ucsf.edu/chimerax/", "description": "The next-generation molecular visualization program, following UCSF Chimera. Source is available [here](https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html)."}, {"name": "DataWarrior", "url": "http://www.openmolecules.org/datawarrior/index.html", "description": "A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence."}]}, {"name": "Command Line Tools", "parent": "Applications", "entries": [{"name": "Open Babel", "url": "http://openbabel.org/wiki/Main_Page", "description": "Chemical toolbox designed to speak the many languages of chemical data."}, {"name": "MayaChemTools", "url": "http://www.mayachemtools.org/index.html", "description": "Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs."}, {"name": "Packmol", "url": "http://m3g.iqm.unicamp.br/packmol/home.shtml", "description": "Initial configurations for molecular dynamics simulations by packing optimization."}, {"name": "BCL::Commons", "url": "http://meilerlab.org/index.php/bclcommons/show/b_apps_id/1", "description": ""}]}, {"name": "Docking", "parent": "Applications", "entries": [{"name": "AutoDock Vina", "url": "http://vina.scripps.edu/", "description": "Molecular docking and virtual screening."}, {"name": "smina", "url": "https://sourceforge.net/projects/smina/", "description": "Customized [AutoDock Vina](http://vina.scripps.edu/) to better support scoring function development and high-performance energy minimization."}]}, {"name": "Virtual Machine", "parent": "Applications", "entries": [{"name": "myChEMBL", "url": "http://chembl.blogspot.com/2015/07/mychembl-20-has-landed.html", "description": "A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)"}, {"name": "3D e-Chem Virtual Machine", "url": "https://github.com/3D-e-Chem/3D-e-Chem-VM", "description": "Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows", "stars": "16"}]}, {"name": "General Purpose", "parent": "Libraries", "entries": [{"name": "RDKit", "url": "http://www.rdkit.org/", "description": "Collection of cheminformatics and machine-learning software written in C++ and Python."}, {"name": "Indigo", "url": "https://github.com/epam/Indigo", "description": "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.", "stars": "270"}, {"name": "CDK (Chemistry Development Kit)", "url": "https://sourceforge.net/projects/cdk/", "description": "Algorithms for structural chemo- and bioinformatics, implemented in Java."}, {"name": "ChemmineR", "url": "https://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html", "description": "Cheminformatics package for analyzing drug-like small molecule data in R."}, {"name": "ChemPy", "url": "https://github.com/bjodah/chempy", "description": "A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)", "stars": "503"}, {"name": "MolecularGraph.jl", "url": "https://github.com/mojaie/MolecularGraph.jl", "description": "A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia", "stars": "183"}, {"name": "datamol", "url": "https://github.com/datamol-org/datamol", "description": "", "stars": "417"}, {"name": "CGRtools", "url": "https://github.com/cimm-kzn/CGRtools", "description": "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.", "stars": "38"}]}, {"name": "Format Checking", "parent": "Libraries", "entries": [{"name": "ChEMBL\\_Structure\\_Pipeline (formerly standardiser)", "url": "https://github.com/chembl/ChEMBL_Structure_Pipeline", "description": "Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.", "stars": "173"}, {"name": "MolVS", "url": "https://github.com/mcs07/MolVS", "description": "Molecule validation and standardization based on [RDKit](http://www.rdkit.org/).", "stars": "143"}, {"name": "rd\\_filters", "url": "https://github.com/PatWalters/rd_filters", "description": "A script to run structural alerts using the RDKit and ChEMBL", "stars": "119"}, {"name": "pdb-tools", "url": "https://github.com/haddocking/pdb-tools", "description": "A swiss army knife for manipulating and editing PDB files.", "stars": "344"}]}, {"name": "Visualization", "parent": "Libraries", "entries": [{"name": "Kekule.js", "url": "http://partridgejiang.github.io/Kekule.js/", "description": "Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers."}, {"name": "3Dmol.js", "url": "https://github.com/3dmol/3Dmol.js", "description": "An object-oriented, webGL based JavaScript library for online molecular visualization.", "stars": "741"}, {"name": "JChemPaint", "url": "https://github.com/JChemPaint/jchempaint", "description": "Chemical 2D structure editor application/applet based on the [Chemistry Development Kit](https://sourceforge.net/projects/cdk/).", "stars": "106"}, {"name": "rdeditor", "url": "https://github.com/EBjerrum/rdeditor", "description": "Simple RDKit molecule editor GUI using PySide.", "stars": "75"}, {"name": "nglviewer", "url": "http://nglviewer.org/nglview/latest/", "description": "Interactive molecular graphics for Jupyter notebooks."}, {"name": "RDKit.js", "url": "https://www.npmjs.com/package/@rdkit/rdkit", "description": "Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics."}]}, {"name": "Molecular Descriptors", "parent": "Libraries", "entries": [{"name": "mordred", "url": "https://github.com/mordred-descriptor/mordred", "description": "Molecular descriptor calculator based on [RDKit](http://www.rdkit.org/).", "stars": "317"}, {"name": "DescriptaStorus", "url": "https://github.com/bp-kelley/descriptastorus", "description": "Descriptor computation(chemistry) and (optional) storage for machine learning.", "stars": "201"}, {"name": "mol2vec", "url": "https://github.com/samoturk/mol2vec", "description": "Vector representations of molecular substructures.", "stars": "239"}, {"name": "Align-it", "url": "http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html#alignit-generating-pharmacophore-points", "description": "Align molecules according their pharmacophores."}, {"name": "Rcpi", "url": "https://nanx.me/Rcpi/index.html", "description": "R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions."}]}, {"name": "Machine Learning", "parent": "Libraries", "entries": [{"name": "DeepChem", "url": "https://github.com/deepchem/deepchem", "description": "Deep learning library for Chemistry based on Tensorflow", "stars": "5k"}, {"name": "Chemprop", "url": "https://github.com/chemprop/chemprop", "description": "Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.", "stars": "1.5k"}, {"name": "ChemML", "url": "https://github.com/hachmannlab/chemml", "description": "ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)", "stars": "148"}, {"name": "olorenchemengine", "url": "https://github.com/Oloren-AI/olorenchemengine", "description": "Molecular property prediction with unified API for diverse models and respresentations,", "stars": "95"}, {"name": "OpenChem", "url": "https://github.com/Mariewelt/OpenChem", "description": "OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.", "stars": "645"}, {"name": "DGL-LifeSci", "url": "https://github.com/awslabs/dgl-lifesci", "description": "DGL-LifeSci is a [DGL](https://www.dgl.ai/)-based package for various applications in life science with graph neural network.", "stars": "667"}, {"name": "chainer-chemistry", "url": "https://github.com/pfnet-research/chainer-chemistry", "description": "A Library for Deep Learning in Biology and Chemistry.", "stars": "604"}, {"name": "pytorch-geometric", "url": "https://pytorch-geometric.readthedocs.io/en/latest/", "description": "A PyTorch library provides implementation of many graph convolution algorithms."}, {"name": "chemmodlab", "url": "https://github.com/jrash/ChemModLab", "description": "A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.", "stars": "12"}, {"name": "Summit", "url": "https://github.com/sustainable-processes/summit", "description": "A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).", "stars": "106"}]}, {"name": "Web APIs", "parent": "Libraries", "entries": [{"name": "webchem", "url": "https://github.com/ropensci/webchem", "description": "Chemical Information from the Web.", "stars": "153"}, {"name": "PubChemPy", "url": "http://pubchempy.readthedocs.io", "description": "Python wrapper for the PubChem PUG REST API."}, {"name": "ChemSpiPy", "url": "http://chemspipy.readthedocs.org", "description": "Python wrapper for the ChemSpider API."}, {"name": "CIRpy", "url": "http://cirpy.readthedocs.org/", "description": "Python wrapper for the [NCI Chemical Identifier Resolver (CIR)](https://cactus.nci.nih.gov/chemical/structure)."}, {"name": "Beaker", "url": "https://github.com/chembl/chembl_beaker", "description": "[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/).", "stars": "47"}, {"name": "chemminetools", "url": "https://github.com/girke-lab/chemminetools", "description": "Open source web framework for small molecule analysis based on Django.", "stars": "35"}, {"name": "ambit", "url": "http://ambit.sourceforge.net/", "description": "offers chemoinformatics functionality via REST web services."}]}, {"name": "Databases", "parent": "Libraries", "entries": [{"name": "razi", "url": "https://github.com/rvianello/razi", "description": "Cheminformatic extension for the SQLAlchemy database.", "stars": "37"}, {"name": "Chemical Translation Service", "url": "https://bitbucket.org/fiehnlab/fiehnlab-cts/src/master/", "description": "Source code of the [Chemical Translation Service](https://cts.fiehnlab.ucdavis.edu/) web service."}]}, {"name": "Docking", "parent": "Libraries", "entries": [{"name": "Rosetta", "url": "https://www.rosettacommons.org/docs/latest/Home", "description": "A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking."}, {"name": "DOCKSTRING", "url": "https://github.com/dockstring/dockstring", "description": "Automates and standardizes ligand preparation for AutoDock Vina.", "stars": "121"}]}, {"name": "Molecular Dynamics", "parent": "Libraries", "entries": [{"name": "Gromacs", "url": "http://www.gromacs.org/", "description": "Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids."}, {"name": "OpenMM", "url": "http://openmm.org/", "description": "High performance toolkit for molecular simulation including extensive language bindings for Python, C, C++, and even Fortran."}, {"name": "NAMD", "url": "https://www.ks.uiuc.edu/Research/namd/", "description": "a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems."}, {"name": "MDTraj", "url": "https://github.com/mdtraj/mdtraj", "description": "Analysis of molecular dynamics trajectories.", "stars": "533"}, {"name": "cclib", "url": "https://github.com/cclib/cclib", "description": "Parsers and algorithms for computational chemistry logfiles.", "stars": "301"}, {"name": "ProDy", "url": "https://github.com/prody/ProDy", "description": "A Python package for protein dynamics analysis", "stars": "379"}]}, {"name": "Others", "parent": "Libraries", "entries": [{"name": "eiR", "url": "https://github.com/girke-lab/eiR", "description": "Accelerated similarity searching of small molecules", "stars": "3"}, {"name": "OPSIN", "url": "https://github.com/dan2097/opsin", "description": "Open Parser for Systematic IUPAC nomenclature", "stars": "126"}, {"name": "Cookiecutter for Computational Molecular Sciences", "url": "https://github.com/MolSSI/cookiecutter-cms", "description": "Python-centric Cookiecutter for Molecular Computational Chemistry Packages by [MolSSL](https://molssi.org/)", "stars": "353"}, {"name": "Auto-QChem", "url": "https://github.com/PrincetonUniversity/auto-qchem", "description": "an automated workflow for the generation and storage of DFT calculations for organic molecules.", "stars": "71"}, {"name": "Gypsum-DL", "url": "https://git.durrantlab.pitt.edu/jdurrant/gypsum_dl", "description": "a program for converting 2D SMILES strings to 3D models."}, {"name": "RDchiral", "url": "https://github.com/connorcoley/rdchiral", "description": "Wrapper for RDKit's RunReactants to improve stereochemistry handling", "stars": "144"}, {"name": "confgen", "url": "https://github.com/Et9797/confgen-webapp", "description": "Webapp for generating conformers", "stars": "4"}, {"name": "Journal of Cheminformatics", "url": "https://jcheminf.biomedcentral.com/", "description": ""}, {"name": "Journal of Chemical Information and Modeling (ACS Publications)", "url": "https://pubs.acs.org/journal/jcisd8", "description": ""}]}, {"name": "Courses", "parent": "Resources", "entries": [{"name": "Learncheminformatics.com", "url": "http://learncheminformatics.com/", "description": "\"Cheminformatics: Navigating the world of chemical data\" courese at Indiana University."}, {"name": "Python for chemoinformatics", "url": "https://github.com/Mishima-syk/py4chemoinformatics", "description": "", "stars": "217"}, {"name": "TeachOpenCADD", "url": "https://github.com/volkamerlab/TeachOpenCADD", "description": "A teaching platform for computer-aided drug design (CADD) using open source packages and data.", "stars": "650"}, {"name": "Cheminformatics OLCC", "url": "https://chem.libretexts.org/Courses/Intercollegiate_Courses/Cheminformatics_OLCC_\\(2019\\", "description": ""}, {"name": "BigChem", "url": "http://bigchem.eu/alllectures", "description": "All lectures of [BigChem](http://bigchem.eu/) (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)"}, {"name": "Molecular modeling course", "url": "https://dasher.wustl.edu/chem478/", "description": "by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis."}, {"name": "Simulation in Chemistry and Biochemistry", "url": "https://dasher.wustl.edu/chem430/", "description": "by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis."}]}, {"name": "Blogs", "parent": "Resources", "entries": [{"name": "Open Source Molecular Modeling", "url": "https://opensourcemolecularmodeling.github.io/README.html", "description": "Updateable catalog of open source molecular modeling software."}, {"name": "PubChem Blog", "url": "https://pubchemblog.ncbi.nlm.nih.gov/", "description": "News, updates and tutorials about [PubChem](https://pubchem.ncbi.nlm.nih.gov/)."}, {"name": "The ChEMBL-og blog", "url": "http://chembl.blogspot.tw/", "description": "Stories and news from Computational Chemical Biology Group at [EMBL-EBI](https://www.ebi.ac.uk/)."}, {"name": "ChEMBL blog", "url": "http://chembl.github.io/", "description": "ChEMBL on GitHub."}, {"name": "SteinBlog", "url": "http://www.steinbeck-molecular.de/steinblog/", "description": "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."}, {"name": "Practical Cheminformatics", "url": "http://practicalcheminformatics.blogspot.com/", "description": "Blog with in-depth examples of practical application of cheminformatics."}, {"name": "So much to do, so little time - Trying to squeeze sense out of chemical data", "url": "http://blog.rguha.net/", "description": "Bolg of [Rajarshi Guha](http://blog.rguha.net/?page_id=8), who is a research scientist at NIH Center for Advancing Translational Science."}, {"name": "Noel O'Blog", "url": "http://baoilleach.blogspot.tw/", "description": "Blog of [Noel O'Boyle](https://www.redbrick.dcu.ie/~noel/), who is a Senior Software Engineer at NextMove Software."}, {"name": "chem-bla-ics", "url": "http://chem-bla-ics.blogspot.tw/", "description": "Blog of [Egon Willighagen](http://egonw.github.io/), who is an assistant professor at Maastricht University."}, {"name": "Asad's Blog", "url": "https://chembioinfo.com/", "description": "Bolg of Syed Asad Rahman, who is a research scientist in the [Thornton group](http://www.ebi.ac.uk/research/thornton) at EMBL-EBI."}, {"name": "steeveslab-blog", "url": "http://asteeves.github.io/", "description": "Some examples using [RDKit](http://www.rdkit.org/)."}, {"name": "Macs in Chemistry", "url": "http://www.macinchem.org/", "description": "Provide a resource for chemists using Apple Macintosh computers."}, {"name": "DrugDiscovery.NET", "url": "http://www.drugdiscovery.net/", "description": "Blog of [Andreas Bender](http://www.andreasbender.de/), who is a Reader for Molecular Informatics at University of Cambridge."}, {"name": "Is life worth living?", "url": "https://iwatobipen.wordpress.com/", "description": "Some examples for cheminformatics libraries."}, {"name": "Cheminformatics 2.0", "url": "https://cheminf20.org/", "description": "Blog of [Alex M. Clark](https://twitter.com/aclarkxyz), a research scientist at Collaborative Drug Discovery."}, {"name": "Depth-First", "url": "https://depth-first.com/", "description": "Blog of [Richard L. Apodaca](https://depth-first.com/about/), a chemist living in La Jolla, California."}, {"name": "Cheminformania", "url": "https://www.cheminformania.com", "description": "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."}]}, {"name": "Books", "parent": "Resources", "entries": [{"name": "Computational Approaches in Cheminformatics and Bioinformatics", "url": "https://books.google.com/books/about/Computational_Approaches_in_Cheminformat.html?id=bLqV4rYQoYsC", "description": "Include insights from public (NIH), academic, and industrial sources at the same time."}, {"name": "Chemoinformatics for Drug Discovery", "url": "https://onlinelibrary.wiley.com/doi/book/10.1002/9781118742785", "description": "Materials about how to use Chemoinformatics strategies to improve drug discovery results."}, {"name": "Molecular Descriptors for Chemoinformatics", "url": "https://onlinelibrary.wiley.com/doi/book/10.1002/9783527628766", "description": "More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties."}, {"name": "deeplearning-biology", "url": "https://github.com/hussius/deeplearning-biology#chemoinformatics-and-drug-discovery-", "description": "Chemoinformatics and drug discovery section in deeplearning-biology repo.", "stars": "1.9k"}, {"name": "awesome-python-chemistry", "url": "https://github.com/lmmentel/awesome-python-chemistry", "description": "Another list focuses on Python stuff related to Chemistry.", "stars": "999"}, {"name": "awesome-small-molecule-ml", "url": "https://github.com/benb111/awesome-small-molecule-ml", "description": "A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.", "stars": "168"}, {"name": "awesome-molecular-docking", "url": "https://github.com/yangnianzu0515/awesome-molecular-docking", "description": "A curated list of molecular docking software, datasets, and other closely related resources.", "stars": "80"}, {"name": "MolSSI Molecular Software Database", "url": "https://molssi.org/software-search/", "description": ""}]}], "name": ""}