Courses & Tutorials
Awesome Cheminformatics – Massive Collection of Resources
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
A curated list of awesome Cheminformatics software, resources, and libraries. Mostly command line based, and free or open-source.
Contents
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. Source is available.
- ChimeraX – The next-generation molecular visualization program, following UCSF Chimera. Source is available here.
- DataWarrior – A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.
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
Docking
- AutoDock Vina – Molecular docking and virtual screening.
- smina – Customized AutoDock Vina to better support scoring function development and high-performance energy minimization.
Virtual Machine
- myChEMBL – A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)
- 3D e-Chem Virtual Machine –
Libraries
General Purpose
- RDKit – Collection of cheminformatics and machine-learning software written in C++ and Python.
- 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) – Algorithms for structural chemo- and bioinformatics, implemented in Java.
- ChemmineR – Cheminformatics package for analyzing drug-like small molecule data in R.
- ChemPy – A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
- MolecularGraph.jl – A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
Format Checking
- ChEMBL_Structure_Pipeline (formerly standardiser) – Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.
- MolVS – Molecule validation and standardization based on RDKit.
- rd_filters – A script to run structural alerts using the RDKit and ChEMBL
Visulization
- Kekule.js – Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
- 3Dmol.js – An object-oriented, webGL based JavaScript library for online molecular visualization.
- JChemPaint – Chemical 2D structure editor application/applet based on the Chemistry Development Kit.
- rdeditor – Simple RDKit molecule editor GUI using PySide.
- nglviewer – Interactive molecular graphics for Jupyter notebooks.
Molecular Descriptors
- mordred – Molecular descriptor calculator based on RDKit.
- DescriptaStorus – Descriptor computation(chemistry) and (optional) storage for machine learning.
- mol2vec – 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.
Machine Learning
- DeepChem – Deep learning library for Chemistry based on Tensorflow
- ChemML – ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
- OpenChem – OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.
- chainer-chemistry – A Library for Deep Learning in Biology and Chemistry.
- pytorch-geometric – A PyTorch library provides implementation of many graph convolution algorithms.
- chemmodlab – A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.
Web APIs
- webchem – 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 NCI Chemical Identifier Resolver (CIR).
- Beaker – RDKit and OSRA in the Bottle on Tornado.
- chemminetools – Open source web framework for small molecule analysis based on Django.
Databases
- razi – Cheminformatic extension for the SQLAlchemy database.
Docking
- Rosetta – A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.
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 – Analysis of molecular dynamics trajectories.
- cclib – Parsers and algorithms for computational chemistry logfiles.
Others
- eiR – Accelerated similarity searching of small molecules
- OPSIN – Open Parser for Systematic IUPAC nomenclature
- Cookiecutter for Computational Molecular Sciences – Python-centric Cookiecutter for Molecular Computational Chemistry Packages by MolSSL
Journals
Resources
Courses
- Learncheminformatics.com – “Cheminformatics: Navigating the world of chemical data” courese at Indiana University.
- Python for chemoinformatics
- TeachOpenCADD – 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 BigChem (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
- Molecular modeling course – by Dr. Jay Ponder, a professor from WashU St.Louis.
- Simulation in Chemistry and Biochemistry – by Dr. Jay Ponder, a professor from WashU St.Louis.
Blogs
- Open Source Molecular Modeling – Updateable catalog of open source molecular modeling software.
- 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.
- 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 Rajarshi Guha, who is a research scientist at NIH Center for Advancing Translational Science.
* Some old blogs 1 2. - Noel O’Blog – Blog of Noel O’Boyle, who is a Senior Software Engineer at NextMove Software.
- chem-bla-ics – Blog of Egon Willighagen, who is an assistant professor at Maastricht University.
- steeveslab-blog – Some examples using RDKit.
- Macs in Chemistry – Provide a resource for chemists using Apple Macintosh computers.
- DrugDiscovery.NET – Blog of Andreas Bender, 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 Alex M. Clark, a research scientist at Collaborative Drug Discovery.
- Depth-First – Blog of Richard L. Apodaca, a chemist living in La Jolla, California.
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.
