Cheminformatics

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

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.

A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)

A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia

Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.

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.

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

Molecule validation and standardization based on RDKit.

A script to run structural alerts using the RDKit and ChEMBL

A swiss army knife for manipulating and editing PDB files.

An object-oriented, webGL based JavaScript library for online molecular visualization.

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

Simple RDKit molecule editor GUI using PySide.

Molecular descriptor calculator based on RDKit.

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

Vector representations of molecular substructures.

Deep learning library for Chemistry based on Tensorflow

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

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

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

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

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

A Library for Deep Learning in Biology and Chemistry.

A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).

Chemical Information from the Web.

RDKit and OSRA in the Bottle on Tornado.

Open source web framework for small molecule analysis based on Django.

Cheminformatic extension for the SQLAlchemy database.

Automates and standardizes ligand preparation for AutoDock Vina.

Analysis of molecular dynamics trajectories.

Parsers and algorithms for computational chemistry logfiles.

A Python package for protein dynamics analysis

Accelerated similarity searching of small molecules

Open Parser for Systematic IUPAC nomenclature

Python-centric Cookiecutter for Molecular Computational Chemistry Packages by MolSSL

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

Wrapper for RDKit's RunReactants to improve stereochemistry handling

Webapp for generating conformers