domain-cheminformatics

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

Some useful RDKit functions

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

Molecule Validation and Standardization

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"

ChEMBL database structure pipelines

Web-based molecule sketcher

Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range

WebGL accelerated JavaScript molecular graphics library

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

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

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

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

The Chemistry Development Kit

Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)

Molsystem provides a general class for handling molecular and periodic systems