awesome-awesomeness/terminal/cheminformatics2

                                                                                 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


Visualization

⟡ PyMOL (https://sourceforge.net/projects/pymol/) - Python-enhanced molecular graphics tool.
⟡ Jmol (http://jmol.sourceforge.net/) - Browser-based HTML5 viewer and stand-alone 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 and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.


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 and 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)


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.


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, 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


General Purpose

⟡ RDKit (http://www.rdkit.org/) - Collection of cheminformatics and machine-learning software written in C++ and 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, C#, and Python wrappers.
⟡ CDK (Chemistry Development Kit) (https://sourceforge.net/projects/cdk/) - Algorithms for structural chemo- and bioinformatics, implemented in 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 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
⟡ 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.


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.


Visualization

⟡ Kekule.js (http://partridgejiang.github.io/Kekule.js/) - Front-end 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 based 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 notebooks.
⟡ RDKit.js (https://www.npmjs.com/package/@rdkit/rdkit) - Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.


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.
⟡ 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.


Machine Learning

⟡ DeepChem (https://github.com/deepchem/deepchem) - Deep learning library for Chemistry based on 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 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 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 in Biology and Chemistry.
⟡ pytorch-geometric (https://pytorch-geometric.readthedocs.io/en/latest/) - A PyTorch library provides implementation of many graph convolution algorithms.
⟡ chemmodlab (https://github.com/jrash/ChemModLab) - A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.
⟡ Summit (https://github.com/sustainable-processes/summit) - A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).


Web APIs

⟡ webchem (https://github.com/ropensci/webchem) - Chemical Information from the Web.
⟡ PubChemPy (http://pubchempy.readthedocs.io) - Python wrapper for the PubChem PUG REST API.
⟡ ChemSpiPy (http://chemspipy.readthedocs.org) - Python wrapper for the ChemSpider API.
⟡ CIRpy (http://cirpy.readthedocs.org/) - 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 web services.


Databases

⟡ razi (https://github.com/rvianello/razi) - Cheminformatic extension for the SQLAlchemy 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.


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.


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, C, C++, and even 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 for computational chemistry logfiles.
⟡ ProDy (https://github.com/prody/ProDy) - A Python package for protein dynamics analysis 


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-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 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.io/README.html) - Updateable catalog of open source molecular modeling software.
⟡ PubChem Blog (https://pubchemblog.ncbi.nlm.nih.gov/) - News, updates and 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.io/) - ChEMBL on 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.io/), who is an assistant professor at Maastricht University.
<!---
⟡ Asad's Blog (https://chembioinfo.com/) - 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 (http://asteeves.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 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.


See Also

⟡ deeplearning-biology (https://github.com/hussius/deeplearning-biology#chemoinformatics-and-drug-discovery-) - Chemoinformatics and drug discovery section in deeplearning-biology repo.
⟡ awesome-python-chemistry (https://github.com/lmmentel/awesome-python-chemistry) - Another list focuses on Python stuff related to Chemistry.
⟡ awesome-small-molecule-ml (https://github.com/benb111/awesome-small-molecule-ml) - A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.
⟡ awesome-molecular-docking (https://github.com/yangnianzu0515/awesome-molecular-docking) - A curated list of molecular docking software, datasets, and other closely related resources.
⟡ MolSSI Molecular Software Database (https://molssi.org/software-search/)
＊Pages created by Tobias Kind, PhD (https://fiehnlab.ucdavis.edu/staff/kind/metabolomics)

License

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cheminformatics Github: https://github.com/hsiaoyi0504/awesome-cheminformatics