A deep learning framework for molecular docking

Message Passing Neural Networks for Molecule Property Prediction

AutoDock Vina

Parameter/topology editor and molecular simulator

bedtools - the swiss army knife for genome arithmetic

Identification of Protein-Ligand Binding Sites using dipolar EPR data

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

Python3 translation of AutoDockTools

Quantum chemistry program executor and IO standardizer (QCSchema).

This package contains deep learning models and related scripts for RoseTTAFold

Making Protein folding accessible to all!

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

Codes for our paper "Programming Biomolecular Interactions with All-Atom Generative Model"

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

IF-SitePred is a method for predicting ligand-binding sites on protein structures. It first generates an embedding for each residue of the protein using the ESM-IF1 (inverse folding) model, then performs point cloud clustering to identify binding site centers.

The second version of the Kraken taxonomic sequence classification system

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

NequIP is a code for building E(3)-equivariant interatomic potentials