Cheminformatics GitHub Repositories

The official sources for the RDKit library

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

Robust, flexible and resource-efficient pipelines using Go and the commandline

A deep learning framework for molecular docking

A tool for retrosynthetic planning

A curated list of Cheminformatics libraries and software.

Web-based molecule sketcher

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

Python package for graph neural networks in chemistry and biology

Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)

The Chemistry Development Kit

Molecular Processing Made Easy.

Interaction Fingerprints for protein-ligand complexes and more

Python wrapper for the PubChem PUG REST API.

Open Drug Discovery Toolkit

Official Python client for accessing ChEMBL API

Curses based ASCII molecule viewer for terminals.

Universal cheminformatics toolkit, utilities and database search tools

Experimental design and (multi-objective) bayesian optimization.

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

No repository description provided.

Deep Reinforcement Learning for de-novo Drug Design

Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.

PyChem-Pro: 100% Python API, fast, flexible & programmable molecular viewer - 2D and 3D, molecular docking pose viewer, cheminformatics library, molecular descriptor calculator, molecular editor, chemical drawing editor, QSAR model developer, and many more...

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

A Javascript cheminformatics toolkit.