interface-cli

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

AutoDock Vina

Biomolecular simulation trajectory/data analysis.

Parameter/topology editor and molecular simulator

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

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

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

Python3 translation of AutoDockTools

The second version of the Kraken taxonomic sequence classification system

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.

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.

Calculation of interatomic interactions in molecular structures

A deep learning framework for molecular docking

Identification of Protein-Ligand Binding Sites using dipolar EPR data

Semiempirical Extended Tight-Binding Program Package

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

A pocket volume analyzer for use in protein modeling.