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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: Aug. 18, 2022, 2:02 a.m.

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

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Visualization

Command Line Tools

Docking

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

14
2
3y 10m
Apache-2.0

General Purpose

Universal cheminformatics libraries, utilities and database search tools

170
66
9m
Apache-2.0

โš— A package useful for chemistry written in Python

292
51
10m
BSD-2-Clause

Graph-based molecule modeling toolkit for cheminformatics

109
24
10m
MIT

Molecular Manipulation Made Easy.

97
9
10m
Apache-2.0

CGRs, molecules and reactions manipulation

10
6
6m
LGPL-3.0

Format Checking

ChEMBL database structure pipelines

80
21
9m
MIT

Molecule Validation and Standardization

84
41
2y 4m
MIT

A script to run structural alerts using the RDKit and ChEMBL

58
21
10m
MIT

A dependency-free cross-platform swiss army knife for PDB files.

170
65
7m
Apache-2.0

Visualization

WebGL accelerated JavaScript molecular graphics library

508
151
9m
n/a

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

82
31
1y 10m
n/a

Simple RDKit molecule editor GUI using PySide

46
14
1y 95d
LGPL-3.0

Molecular Descriptors

a molecular descriptor calculator

186
59
1y 6m
BSD-3-Clause

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

104
36
9m
n/a

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

157
75
1y 81d
BSD-3-Clause

Machine Learning

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

3.24K
1.08K
9m
MIT

ChemML is a machine learning and informatics program suite for the chemical and materials sciences.

105
25
9m
BSD-3-Clause

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

404
75
1y 94d
MIT

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

505
125
1y 9m
MIT

chemmodlab: A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models

11
8
11m
GPL-3.0

Optimising chemical reactions using machine learning

48
8
11m
MIT

Web APIs

Chemical Information from the Web

104
35
9m
n/a

RDKit wrapper

33
21
1y 40d
n/a

ChemMine Tools: open source web framework for small molecule analysis

34
14
11m
n/a

Databases

A cheminformatics extension for the SQLAlchemy database toolkit.

24
7
2y 119d
n/a

Docking

Molecular Dynamics

An open library for the analysis of molecular dynamics trajectories

350
208
9m
LGPL-2.1

Parsers and algorithms for computational chemistry logfiles

204
122
9m
BSD-3-Clause

Others

Accelerated similarity searching of small molecules (bioconductor package)

2
0
1y 4m
n/a

Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion

49
16
10m
MIT

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

226
54
1y 8d
MIT

Journals

Courses

Python for chemoinformatics

158
60
1y 53d
n/a

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

269
92
9m
CC-BY-4.0

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

Blogs

Christoph Steinbeck, who is the head of cheminformatics and metabolism at the EMBL-EBI.

Rajarshi Guha, who is a research scientist at NIH Center for Advancing Translational Science.

Noel O'Boyle, who is a Senior Software Engineer at NextMove Software.

Egon Willighagen, who is an assistant professor at Maastricht University.

Andreas Bender, who is a Reader for Molecular Informatics at University of Cambridge.

Alex M. Clark, a research scientist at Collaborative Drug Discovery.

Richard L. Apodaca, a chemist living in La Jolla, California.

Ph.D, Esben Jannik Bjerrum, who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.

Books

See Also

A list of deep learning implementations in biology

1.67K
442
1y 4m
n/a

A curated list of Python packages related to chemistry

494
110
10m
n/a