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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.

Last Update: Dec. 2, 2020, 12:04 p.m.

Thank you hsiaoyi0504 & contributors
View Topic on GitHub:
hsiaoyi0504/awesome-cheminformatics

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Visualization

Python-enhanced molecular graphics tool.

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.

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

Molecular docking and virtual screening.

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

12
2
2y 67d
Apache-2.0

A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)

General Purpose

Universal cheminformatics libraries, utilities and database search tools

135
50
7d
n/a

โš— A package useful for chemistry written in Python

226
45
8d
BSD-2-Clause

Graph-based molecule modeling toolkit for cheminformatics

46
11
2d
MIT

Cheminformatics and Machine Learning Software.

Algorithms for structural chemo- and bioinformatics, implemented in Java.

Cheminformatics package for analyzing drug-like small molecule data in R.

Format Checking

Molecule Validation and Standardization

70
34
1y 8m
MIT

A script to run structural alerts using the RDKit and ChEMBL

41
13
4m
MIT

Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.

Visulization

WebGL accelerated JavaScript molecular graphics library

417
125
3d
n/a

Chemical 2D structure editor application/applet based on the Chemistry Development Kit

69
28
50d
n/a

Simple RDKit molecule editor GUI using PySide

34
10
1y 8m
LGPL-3.0

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

131
42
1y 6m
BSD-3-Clause

Descriptor computation(chemistry) and (optional) storage for machine learning

62
24
6m
n/a

Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures

122
53
11m
BSD-3-Clause

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

2.56K
867
7d
MIT

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

281
36
21d
MIT

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

440
118
40d
MIT

A PyTorch library provides implementation of many graph convolution algorithms.

Web APIs

Chemical Information from the Web

84
31
34d
n/a

RDKit and OSRA in the Bottle on Tornado

24
21
4m
n/a

ChemMine Tools: open source web framework for small molecule analysis

30
11
9d
n/a

Python wrapper for the PubChem PUG REST API.

Python wrapper for the ChemSpider API.

Databases

A cheminformatics extension for the SQLAlchemy database toolkit.

23
6
7m
n/a

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

298
188
20d
LGPL-2.1

Parsers and algorithms for computational chemistry logfiles

178
111
9d
BSD-3-Clause

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)

1
0
49d
n/a

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

169
41
15d
MIT

Open Parser for Systematic IUPAC nomenclature

Journals

Courses

Python for chemoinformatics

132
42
9m
n/a

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

166
53
8d
CC-BY-4.0

Cheminformatics: Navigating the world of chemical data" courese at Indiana University.

3A_Chem_4399%2F%2F5399) - ChemInformatics course (Spring 2017) of University of Arkansas at Little Rock by Robert Belford

All lectures of BigChem (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)

Blogs

Updateable catalog of open source molecular modeling software.

News, updates and tutorials about PubChem.

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.

1

2](http://www.rguha.net/index.html).

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

1.5K
404
11m
n/a

A curated list of Python packages related to chemistry

367
96
6d
n/a