interface-cli

Cryptic binding pocket discovery from conformational ensembles. Open-source, reproducible, size-robust benchmarks against fpocket, PocketMiner and CryptoBench.

AutoDock Vina

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

Python3 translation of AutoDockTools

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

Parameter/topology editor and molecular simulator

Biomolecular simulation trajectory/data analysis.

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

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

Semiempirical Extended Tight-Binding Program Package

Identification of Protein-Ligand Binding Sites using dipolar EPR data

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

This package contains deep learning models and related scripts for RoseTTAFold

Quantum chemistry program executor and IO standardizer (QCSchema).

Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 oral]

The second version of the Kraken taxonomic sequence classification system

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.

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

Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.