awesome-cheminformatics

Python-enhanced molecular graphics tool

Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D

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. is available

The next-generation molecular visualization program, following UCSF Chimera. Source is available

A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence

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

Molecular docking and virtual screening

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

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

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

Algorithms for structural chemo- and bioinformatics, implemented in Java

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

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

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

rdeditor

Simple RDKit molecule editor GUI using PySide

Interactive molecular graphics for Jupyter notebooks

Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics

mordred

Molecular descriptor calculator based on

DescriptaStorus

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

mol2vec

Vector representations of molecular substructures

Align molecules according their pharmacophores

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 -based package for various applications in life science with graph neural network

chainer-chemistry

A Library for Deep Learning in Biology and Chemistry

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

Python wrapper for the PubChem PUG REST API

Python wrapper for the ChemSpider API

Python wrapper for the

Beaker

and in the on

chemminetools

Open source web framework for small molecule analysis based on Django

offers chemoinformatics functionality via REST web services

razi

Cheminformatic extension for the SQLAlchemy database

Source code of the web service

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

DOCKSTRING

Automates and standardizes ligand preparation for AutoDock Vina

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

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

Auto-QChem

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

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

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

TeachOpenCADD

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

Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of Arkansas at Little Rock by Robert Belford

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

by Dr. , a professor from WashU St.Louis

by Dr. , a professor from WashU St.Louis

Updateable catalog of open source molecular modeling software

News, updates and tutorials about

Stories and news from Computational Chemical Biology Group at

ChEMBL on GitHub

Blog of , who is the head of cheminformatics and metabolism at the EMBL-EBI

Blog with in-depth examples of practical application of cheminformatics

Bolg of , who is a research scientist at NIH Center for Advancing Translational Science.  * Some old blogs

Blog of , who is a Senior Software Engineer at NextMove Software

Blog of , who is an assistant professor at Maastricht University

Some examples using

Provide a resource for chemists using Apple Macintosh computers

Blog of , who is a Reader for Molecular Informatics at University of Cambridge

Some examples for cheminformatics libraries

Blog of , a research scientist at Collaborative Drug Discovery

Blog of , a chemist living in La Jolla, California

Blog of , who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca

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

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

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