Track Awesome Cheminformatics Updates Daily
A curated list of Cheminformatics libraries and software.
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Mar 15, 2024
Libraries / Machine Learning
- Chemprop (⭐1.5k) - Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
Libraries / Docking
- DOCKSTRING (⭐121) - Automates and standardizes ligand preparation for AutoDock Vina.
Jan 05, 2023
Libraries / Web APIs
- ambit - offers chemoinformatics functionality via REST web services.
Libraries / Databases
- Chemical Translation Service - Source code of the Chemical Translation Service web service.
Libraries / Molecular Dynamics
- ProDy (⭐379) - A Python package for protein dynamics analysis
Libraries / Others
- Gypsum-DL - a program for converting 2D SMILES strings to 3D models.
- RDchiral (⭐144) - Wrapper for RDKit's RunReactants to improve stereochemistry handling
- confgen (⭐4) - Webapp for generating conformers
Dec 22, 2022
See Also / Books
- awesome-molecular-docking (⭐80) - A curated list of molecular docking software, datasets, and other closely related resources.
Dec 11, 2022
Libraries / Machine Learning
- DGL-LifeSci (⭐667) - DGL-LifeSci is a DGL-based package for various applications in life science with graph neural network.
Aug 30, 2022
Libraries / Machine Learning
- olorenchemengine (⭐95) - Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.
Jun 17, 2022
Libraries / Others
- Auto-QChem (⭐71) - an automated workflow for the generation and storage of DFT calculations for organic molecules.
Feb 06, 2022
Libraries / General Purpose
- CGRtools (⭐38) - 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.
Jan 06, 2022
See Also / Books
- awesome-small-molecule-ml (⭐168) - A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.
Dec 22, 2021
Libraries / Format Checking
- pdb-tools (⭐344) - A swiss army knife for manipulating and editing PDB files.
Sep 17, 2021
Resources / Blogs
- Cheminformania - Blog of Ph.D, Esben Jannik Bjerrum, who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.
Aug 31, 2021
Libraries / General Purpose
- datamol (⭐417): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
Libraries / Visualization
- RDKit.js - Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.
Jun 15, 2021
Libraries / Machine Learning
- Summit (⭐106) - A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).
Dec 26, 2020
Libraries / Format Checking
- ChEMBL_Structure_Pipeline (formerly standardiser) (⭐173) - Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.
Libraries / Machine Learning
- ChemML (⭐148) - ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
- chemmodlab (⭐12) - A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.
Libraries / Others
- OPSIN (⭐126) - Open Parser for Systematic IUPAC nomenclature
Resources / Courses
- Cheminformatics OLCC - Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of Arkansas at Little Rock by Robert Belford
Jul 14, 2020
Libraries / Molecular Descriptors
- DescriptaStorus (⭐201) - Descriptor computation(chemistry) and (optional) storage for machine learning.
Libraries / Docking
- Rosetta - A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.
Jun 12, 2020
Libraries / General Purpose
- MolecularGraph.jl (⭐183) - A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
May 27, 2020
Resources / Blogs
- Cheminformatics 2.0 - Blog of Alex M. Clark, a research scientist at Collaborative Drug Discovery.
- Depth-First - Blog of Richard L. Apodaca, a chemist living in La Jolla, California.
See Also / Books
May 21, 2020
Libraries / Web APIs
- CIRpy - Python wrapper for the NCI Chemical Identifier Resolver (CIR).
- chemminetools (⭐35) - Open source web framework for small molecule analysis based on Django.
May 19, 2020
Libraries / General Purpose
- ChemPy (⭐503) - A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
May 17, 2020
Libraries / Others
- eiR (⭐3) - Accelerated similarity searching of small molecules
May 16, 2020
Libraries / Machine Learning
- OpenChem (⭐645) - OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.
May 13, 2020
Libraries / Molecular Dynamics
- NAMD - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
May 10, 2020
Applications / Command Line Tools
Apr 26, 2020
Libraries / Others
- Cookiecutter for Computational Molecular Sciences (⭐353) - Python-centric Cookiecutter for Molecular Computational Chemistry Packages by MolSSL
Resources / Courses
Apr 20, 2020
Resources / Courses
- Simulation in Chemistry and Biochemistry - by Dr. Jay Ponder, a professor from WashU St.Louis.
Mar 23, 2020
Resources / Courses
- Molecular modeling course - by Dr. Jay Ponder, a professor from WashU St.Louis.
Mar 13, 2020
Applications / Visualization
- Chimera - Highly extensible program for interactive molecular visualization and analysis. Source is available.
- ChimeraX - The next-generation molecular visualization program, following UCSF Chimera. Source is available here.
Applications / Virtual Machine
- myChEMBL - A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)
Mar 12, 2020
Libraries / Visualization
- nglviewer - Interactive molecular graphics for Jupyter notebooks.
Feb 11, 2020
Applications / Virtual Machine
- 3D e-Chem Virtual Machine (⭐16) - Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows
Jan 29, 2020
Resources / Books
- Molecular Descriptors for Chemoinformatics - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.
Jan 28, 2020
Libraries / Molecular Descriptors
- Rcpi - R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.
Jan 08, 2020
Libraries / Format Checking
- rd_filters (⭐119) - A script to run structural alerts using the RDKit and ChEMBL
Libraries / Machine Learning
- DeepChem (⭐5k) - Deep learning library for Chemistry based on Tensorflow
- pytorch-geometric - A PyTorch library provides implementation of many graph convolution algorithms.
Jan 05, 2020
Applications / Visualization
- DataWarrior - A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.
Dec 16, 2019
Resources / Courses
- BigChem - All lectures of BigChem (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
Oct 29, 2019
Libraries / Visualization
- 3Dmol.js (⭐741) - An object-oriented, webGL based JavaScript library for online molecular visualization.
Oct 24, 2019
Resources / Blogs
- Is life worth living? - Some examples for cheminformatics libraries.
Sep 18, 2019
Resources / Blogs
- DrugDiscovery.NET - Blog of Andreas Bender, who is a Reader for Molecular Informatics at University of Cambridge.
Sep 06, 2019
Resources / Courses
- TeachOpenCADD (⭐650) - A teaching platform for computer-aided drug design (CADD) using open source packages and data.
Jun 19, 2019
Applications / Command Line Tools
- Packmol - Initial configurations for molecular dynamics simulations by packing optimization.
Jun 11, 2019
Libraries / Machine Learning
- chainer-chemistry (⭐604) - A Library for Deep Learning in Biology and Chemistry.
Feb 28, 2019
Libraries / Molecular Descriptors
- Align-it - Align molecules according their pharmacophores.
Resources / Blogs
- Open Source Molecular Modeling - Updateable catalog of open source molecular modeling software.
- Noel O'Blog - Blog of Noel O'Boyle, who is a Senior Software Engineer at NextMove Software.
See Also / Books
- deeplearning-biology (⭐1.9k) - Chemoinformatics and drug discovery section in deeplearning-biology repo.
Dec 15, 2018
Libraries / Visualization
- rdeditor (⭐75) - Simple RDKit molecule editor GUI using PySide.
Dec 10, 2018
Journals / Others
Aug 24, 2018
Resources / Blogs
- Practical Cheminformatics - Blog with in-depth examples of practical application of cheminformatics.
Aug 09, 2018
Resources / Books
- Chemoinformatics for Drug Discovery - Materials about how to use Chemoinformatics strategies to improve drug discovery results.
May 28, 2018
Resources / Books
- Computational Approaches in Cheminformatics and Bioinformatics - Include insights from public (NIH), academic, and industrial sources at the same time.
May 15, 2018
Libraries / Databases
- razi (⭐37) - Cheminformatic extension for the SQLAlchemy database.
May 08, 2018
Libraries / General Purpose
- CDK (Chemistry Development Kit) - Algorithms for structural chemo- and bioinformatics, implemented in Java.
Libraries / Visualization
- JChemPaint (⭐106) - Chemical 2D structure editor application/applet based on the Chemistry Development Kit.
May 04, 2018
Applications / Command Line Tools
- MayaChemTools - Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs.
Libraries / Molecular Dynamics
- cclib (⭐301) - Parsers and algorithms for computational chemistry logfiles.
May 03, 2018
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.
Applications / Command Line Tools
- Open Babel - Chemical toolbox designed to speak the many languages of chemical data.
Applications / Docking
- AutoDock Vina - Molecular docking and virtual screening.
- smina - Customized AutoDock Vina to better support scoring function development and high-performance energy minimization.
Libraries / General Purpose
- RDKit - Collection of cheminformatics and machine-learning software written in C++ and Python.
- Indigo (⭐270) - 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.
- ChemmineR - Cheminformatics package for analyzing drug-like small molecule data in R.
Libraries / Format Checking
- MolVS (⭐143) - Molecule validation and standardization based on RDKit.
Libraries / Visualization
- Kekule.js - Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
Libraries / Molecular Descriptors
- mordred (⭐317) - Molecular descriptor calculator based on RDKit.
- mol2vec (⭐239) - Vector representations of molecular substructures.
Libraries / Web APIs
- webchem (⭐153) - Chemical Information from the Web.
- Beaker (⭐47) - RDKit and OSRA in the Bottle on Tornado.
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.
- MDTraj (⭐533) - Analysis of molecular dynamics trajectories.
Resources / Courses
- Learncheminformatics.com - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.
Resources / Blogs
- PubChem Blog - News, updates and tutorials about PubChem.
- The ChEMBL-og blog - Stories and news from Computational Chemical Biology Group at EMBL-EBI.
- ChEMBL blog - ChEMBL on GitHub.
- SteinBlog - Blog of Christoph Steinbeck, who is the head of cheminformatics and metabolism at the EMBL-EBI.
- chem-bla-ics - Blog of Egon Willighagen, who is an assistant professor at Maastricht University.
- steeveslab-blog - Some examples using RDKit.
May 02, 2018
Libraries / Web APIs
- PubChemPy - Python wrapper for the PubChem PUG REST API.
- ChemSpiPy - Python wrapper for the ChemSpider API.
Resources / Blogs
- So much to do, so little time - Trying to squeeze sense out of chemical data - Bolg of Rajarshi Guha, who is a research scientist at NIH Center for Advancing Translational Science. * Some old blogs 1 2.
- Macs in Chemistry - Provide a resource for chemists using Apple Macintosh computers.
See Also / Books
- awesome-python-chemistry (⭐999) - Another list focuses on Python stuff related to Chemistry.