What are cheminformatics resources?

Photo by Christina Victoria Craft on Unsplash

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 chemoinformatics analysis of chemical compound properties.

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.

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.

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
• datamol: — Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
• 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) — 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
• pdb-tools — A swiss army knife for manipulating and editing PDB files.

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 — 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.
• RDKit.js — Official JavaScript distribution of cheminformatics functionality from the RDKit — a C++ library for cheminformatics.

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.
• Summit — A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).

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.
• ZINC 15 database

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.
• Cheminformania — Blog of Ph.D, Esben Jannik Bjerrum, who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.

I hope these resources would be useful for you, please follow our Medium account and keep in touch with me (Melanee) on my GitHub.

Resource:

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

Writer: Melanee

Contact Melanee: https://github.com/Melanee-Melanee

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