domain-cheminformatics

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

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

Some useful RDKit functions

Molecule Validation and Standardization

Universal cheminformatics toolkit, utilities and database search tools

Official Python client for accessing ChEMBL API

A package to identify matched molecular pairs and use them to predict property changes.

This repository contains code for the paper: Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES

The Chemistry Development Kit

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

A tool for retrosynthetic planning

Molecular Processing Made Easy.

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).

A Pharmacophore MultiToolkit designed to simplify and streamline the detection, generation, analysis, comparison, and application of pharmacophore models in drug-design strategies.

Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping

Benchmarks for generative chemistry

[Sci. Adv. 2026] The official repository of our paper "Steering Semi-flexible Molecular Diffusion Model for Structure-Based Drug Design with Reinforcement Learning"

Library for reading and writing chemistry files

Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.