awesome-cheminformatics
Cheminformatics toolkit
A curated collection of Cheminformatics software and libraries for various tasks such as visualization, docking, and molecular analysis.
A curated list of Cheminformatics libraries and software.
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last commit: 10 months ago
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awesomeawesome-listbioinformaticscheminformaticschemistry
Awesome Cheminformatics / 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. is available | ||
| ChimeraX | The next-generation molecular visualization program, following UCSF Chimera. Source is available | ||
| DataWarrior | A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence | ||
Awesome Cheminformatics / Applications / 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 | |||
Awesome Cheminformatics / Applications / Docking | |||
| AutoDock Vina | Molecular docking and virtual screening | ||
| smina | Customized to better support scoring function development and high-performance energy minimization | ||
Awesome Cheminformatics / Applications / Virtual Machine | |||
| myChEMBL | A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit) | ||
| 3D e-Chem Virtual Machine | 16 | over 6 years ago | Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows |
Awesome Cheminformatics / Libraries / General Purpose | |||
| RDKit | Collection of cheminformatics and machine-learning software written in C++ and Python | ||
| Indigo | 318 | about 1 month ago | 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) | Algorithms for structural chemo- and bioinformatics, implemented in Java | ||
| ChemmineR | Cheminformatics package for analyzing drug-like small molecule data in R | ||
| ChemPy | 560 | 4 months ago | A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry) |
| MolecularGraph.jl | 202 | about 2 months ago | A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia |
| datamol | 476 | 7 months ago | : - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit |
| CGRtools | 43 | about 2 years ago | 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 |
Awesome Cheminformatics / Libraries / Format Checking | |||
| ChEMBL_Structure_Pipeline (formerly standardiser) | 197 | 5 months ago | Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises |
| MolVS | 163 | almost 5 years ago | Molecule validation and standardization based on |
| rd_filters | 132 | over 1 year ago | A script to run structural alerts using the RDKit and ChEMBL |
| pdb-tools | 391 | 5 months ago | A swiss army knife for manipulating and editing PDB files |
Awesome Cheminformatics / Libraries / Visualization | |||
| Kekule.js | Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers | ||
| 3Dmol.js | 825 | about 2 months ago | An object-oriented, webGL based JavaScript library for online molecular visualization |
| JChemPaint | 115 | 7 months ago | Chemical 2D structure editor application/applet based on the |
| rdeditor | 137 | 4 months ago | Simple RDKit molecule editor GUI using PySide |
| nglviewer | Interactive molecular graphics for Jupyter notebooks | ||
| RDKit.js | Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics | ||
Awesome Cheminformatics / Libraries / Molecular Descriptors | |||
| mordred | 376 | 12 months ago | Molecular descriptor calculator based on |
| DescriptaStorus | 237 | 3 months ago | Descriptor computation(chemistry) and (optional) storage for machine learning |
| mol2vec | 258 | over 2 years ago | Vector representations of molecular substructures |
| Align-it | Align molecules according their pharmacophores | ||
| Rcpi | R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions | ||
Awesome Cheminformatics / Libraries / Machine Learning | |||
| DeepChem | 5,599 | about 1 month ago | Deep learning library for Chemistry based on Tensorflow |
| Chemprop | 1,827 | about 2 months ago | Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation |
| ChemML | 163 | over 1 year ago | ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow) |
| olorenchemengine | 98 | over 1 year ago | Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning |
| OpenChem | 684 | about 1 year ago | OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend |
| DGL-LifeSci | 734 | about 1 year ago | DGL-LifeSci is a -based package for various applications in life science with graph neural network |
| chainer-chemistry | 641 | over 1 year ago | A Library for Deep Learning in Biology and Chemistry |
| pytorch-geometric | A PyTorch library provides implementation of many graph convolution algorithms | ||
| chemmodlab | 15 | over 1 year ago | A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R |
| Summit | 124 | 5 months ago | A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks) |
Awesome Cheminformatics / Libraries / Web APIs | |||
| webchem | 164 | 11 months ago | Chemical Information from the Web |
| PubChemPy | Python wrapper for the PubChem PUG REST API | ||
| ChemSpiPy | Python wrapper for the ChemSpider API | ||
| CIRpy | Python wrapper for the | ||
| Beaker | 49 | 9 months ago | and in the on |
| chemminetools | 36 | about 2 years ago | Open source web framework for small molecule analysis based on Django |
| ambit | offers chemoinformatics functionality via REST web services | ||
Awesome Cheminformatics / Libraries / Databases | |||
| razi | 38 | almost 2 years ago | Cheminformatic extension for the SQLAlchemy database |
| Chemical Translation Service | Source code of the web service | ||
Awesome Cheminformatics / Libraries / Docking | |||
| Rosetta | A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking | ||
| DOCKSTRING | 161 | about 2 months ago | Automates and standardizes ligand preparation for AutoDock Vina |
Awesome Cheminformatics / Libraries / 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 | ||
| MDTraj | 602 | about 1 month ago | Analysis of molecular dynamics trajectories |
| cclib | 339 | about 1 month ago | Parsers and algorithms for computational chemistry logfiles |
| ProDy | 439 | about 1 month ago | A Python package for protein dynamics analysis |
Awesome Cheminformatics / Libraries / Others | |||
| eiR | 3 | almost 2 years ago | Accelerated similarity searching of small molecules |
| OPSIN | 161 | 3 months ago | Open Parser for Systematic IUPAC nomenclature |
| Cookiecutter for Computational Molecular Sciences | 404 | 5 months ago | Python-centric Cookiecutter for Molecular Computational Chemistry Packages by |
| Auto-QChem | 88 | 3 months ago | an automated workflow for the generation and storage of DFT calculations for organic molecules |
| Gypsum-DL | a program for converting 2D SMILES strings to 3D models | ||
| RDchiral | 155 | over 1 year ago | Wrapper for RDKit's RunReactants to improve stereochemistry handling |
| confgen | 5 | about 1 year ago | Webapp for generating conformers |
Awesome Cheminformatics / Journals | |||
| Journal of Cheminformatics | |||
| Journal of Chemical Information and Modeling (ACS Publications) | |||
Awesome Cheminformatics / Resources / Courses | |||
| Learncheminformatics.com | "Cheminformatics: Navigating the world of chemical data" courese at Indiana University | ||
| Python for chemoinformatics | 223 | over 3 years ago | |
| TeachOpenCADD | 792 | 6 months ago | A teaching platform for computer-aided drug design (CADD) using open source packages and data |
| 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 (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.) | ||
| Molecular modeling course | by Dr. , a professor from WashU St.Louis | ||
| Simulation in Chemistry and Biochemistry | by Dr. , a professor from WashU St.Louis | ||
Awesome Cheminformatics / Resources / Blogs | |||
| Open Source Molecular Modeling | Updateable catalog of open source molecular modeling software | ||
| PubChem Blog | News, updates and tutorials about | ||
| The ChEMBL-og blog | Stories and news from Computational Chemical Biology Group at | ||
| ChEMBL blog | ChEMBL on GitHub | ||
| SteinBlog | Blog of , 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 , who is a research scientist at NIH Center for Advancing Translational Science. * Some old blogs | ||
| Noel O'Blog | Blog of , who is a Senior Software Engineer at NextMove Software | ||
| chem-bla-ics | Blog of , who is an assistant professor at Maastricht University | ||
| steeveslab-blog | Some examples using | ||
| Macs in Chemistry | Provide a resource for chemists using Apple Macintosh computers | ||
| DrugDiscovery.NET | Blog of , 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 , a research scientist at Collaborative Drug Discovery | ||
| Depth-First | Blog of , a chemist living in La Jolla, California | ||
| Cheminformania | Blog of , who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca | ||
Awesome Cheminformatics / Resources / Books | |||
| Computational Approaches in Cheminformatics and Bioinformatics | Include insights from public (NIH), academic, and industrial sources at the same time | ||
| Chemoinformatics for Drug Discovery | Materials about how to use Chemoinformatics strategies to improve drug discovery results | ||
| Molecular Descriptors for Chemoinformatics | More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties | ||
Awesome Cheminformatics / See Also | |||
| deeplearning-biology | 2,026 | 5 months ago | Chemoinformatics and drug discovery section in deeplearning-biology repo |
| awesome-python-chemistry | 1,152 | 3 months ago | Another list focuses on Python stuff related to Chemistry |
| awesome-small-molecule-ml | 207 | about 1 year ago | A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery |
| awesome-molecular-docking | 94 | almost 2 years ago | A curated list of molecular docking software, datasets, and other closely related resources |
| MolSSI Molecular Software Database | ＊ | ||
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