RDKit

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

Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.

Molecule validation and standardization based on [RDKit](http://www.rdkit.org/).

Deep learning framework for molecular docking extending AutoDock Vina with convolutional neural network scoring functions, achieving superior virtual screening enrichment and pose prediction across diverse target classes; widely adopted in pharmaceutical structure-based drug design (J. Cheminformatics, 915+ stars, actively maintained)

Interaction Fingerprints for protein-ligand complexes and more.