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.

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

AutoDock Vina

Molecular docking and virtual screening.

smina

Customized AutoDock Vina to better support scoring function development and high-performance energy minimization.

myChEMBL

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

3D e-Chem Virtual Machine

Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows

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.

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.

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.

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.

DeepChem

Deep learning library for Chemistry based on Tensorflow

Chemprop

Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.

ChemML

ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)

olorenchemengine

Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.

OpenChem

OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.

DGL-LifeSci

DGL-LifeSci is a DGL-based package for various applications in life science with graph neural network.

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).

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.

ambit

offers chemoinformatics functionality via REST web services.

razi

Cheminformatic extension for the SQLAlchemy database.

Chemical Translation Service

Source code of the Chemical Translation Service web service.

Rosetta

A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.

DOCKSTRING

Automates and standardizes ligand preparation for AutoDock Vina.

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.

ProDy

A Python package for protein dynamics analysis

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

Auto-QChem

an automated workflow for the generation and storage of DFT calculations for organic molecules.

Gypsum-DL

a program for converting 2D SMILES strings to 3D models.

RDchiral

Wrapper for RDKit's RunReactants to improve stereochemistry handling

confgen

Webapp for generating conformers

Journal of Cheminformatics

Journal of Chemical Information and Modeling (ACS Publications)

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.

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.

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.

deeplearning-biology

Chemoinformatics and drug discovery section in deeplearning-biology repo.

awesome-python-chemistry

Another list focuses on Python stuff related to Chemistry.

awesome-small-molecule-ml

A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.

awesome-molecular-docking

A curated list of molecular docking software, datasets, and other closely related resources.

MolSSI Molecular Software Database

＊Pages created by Tobias Kind, PhD