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. Please feel
free to contribute !
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
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
### 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.
-
Summit - A
python package for optimizing chemical reactions using machine learning
(contains 10 algorithms + several benchmarks).
### Web APIs
### 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
Journals
Resources
Courses
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
## See Also
License
