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Awesome Cheminformatics
A curated list of Cheminformatics libraries and software.
Here you can see meta information about this topic like the time we last updated this page, the original creator of the awesome list and a link to the original GitHub repository.
Thank you hsiaoyi0504 & contributors
View Topic on GitHub:
hsiaoyi0504/awesome-cheminformatics
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Visualization
Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D.
Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Highly extensible program for interactive molecular visualization and analysis. Source is available.
The next-generation molecular visualization program, following UCSF Chimera. Source is available here.
A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.
Command Line Tools
A chemical toolbox designed to speak the many languages of chemical data.
Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs.
Initial configurations for molecular dynamics simulations by packing optimization.
Docking
Customized AutoDock Vina to better support scoring function development and high-performance energy minimization.
Virtual Machine
Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows
A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)
General Purpose
Universal cheminformatics libraries, utilities and database search tools
⚗ A package useful for chemistry written in Python
Graph-based molecule modeling toolkit for cheminformatics
Algorithms for structural chemo- and bioinformatics, implemented in Java.
Cheminformatics package for analyzing drug-like small molecule data in R.
Format Checking
ChEMBL database structure pipelines
Molecule Validation and Standardization
A script to run structural alerts using the RDKit and ChEMBL
Visulization
WebGL accelerated JavaScript molecular graphics library
Chemical 2D structure editor application/applet based on the Chemistry Development Kit
Simple RDKit molecule editor GUI using PySide
Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
Interactive molecular graphics for Jupyter notebooks.
Molecular Descriptors
a molecular descriptor calculator
Descriptor computation(chemistry) and (optional) storage for machine learning
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
Align molecules according their pharmacophores.
R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.
Machine Learning
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
ChemML is a machine learning and informatics program suite for the chemical and materials sciences.
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
chemmodlab: A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models
A PyTorch library provides implementation of many graph convolution algorithms.
Web APIs
Chemical Information from the Web
RDKit and OSRA in the Bottle on Tornado
ChemMine Tools: open source web framework for small molecule analysis
Databases
A cheminformatics extension for the SQLAlchemy database toolkit.
Docking
A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.
Molecular Dynamics
An open library for the analysis of molecular dynamics trajectories
Parsers and algorithms for computational chemistry logfiles
Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
High performance toolkit for molecular simulation including extensive language bindings for Python, C, C++, and even Fortran.
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Others
Accelerated similarity searching of small molecules (bioconductor package)
Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion
Python-centric Cookiecutter for Molecular Computational Chemistry Packages
Journals
Courses
Python for chemoinformatics
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
Cheminformatics: Navigating the world of chemical data" courese at Indiana University.
All lectures of BigChem (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
by Dr. Jay Ponder, a professor from WashU St.Louis.
by Dr. Jay Ponder, a professor from WashU St.Louis.
Blogs
Updateable catalog of open source molecular modeling software.
Stories and news from Computational Chemical Biology Group at EMBL-EBI.
Blog of Christoph Steinbeck, who is the head of cheminformatics and metabolism at the EMBL-EBI.
Blog with in-depth examples of practical application of cheminformatics.
Bolg of Rajarshi Guha, who is a research scientist at NIH Center for Advancing Translational Science.
Blog of Noel O'Boyle, who is a Senior Software Engineer at NextMove Software.
Blog of Egon Willighagen, who is an assistant professor at Maastricht University.
Bolg of Syed Asad Rahman, who is a research scientist in the Thornton group at EMBL-EBI.
Provide a resource for chemists using Apple Macintosh computers.
Blog of Andreas Bender, who is a Reader for Molecular Informatics at University of Cambridge.
Some examples for cheminformatics libraries.
Blog of Alex M. Clark, a research scientist at Collaborative Drug Discovery.
Blog of Richard L. Apodaca, a chemist living in La Jolla, California.
Books
Include insights from public (NIH), academic, and industrial sources at the same time.
Materials about how to use Chemoinformatics strategies to improve drug discovery results.
More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.
See Also
A list of deep learning implementations in biology
A curated list of Python packages related to chemistry