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

Biomolecular simulation trajectory/data analysis.

Parameter/topology editor and molecular simulator

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

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

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

A deep learning framework for molecular docking

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

Standalone charge assignment from Espaloma framework.

Message Passing Neural Networks for Molecule Property Prediction

doujinshi-dl-gui is a graphical user interface for interacting with RicterZ's doujinshi-dl command-line tool. It provides a more user-friendly way to configure and run doujinshi-dl commands without needing to use the command line directly.

Quantum chemistry program executor and IO standardizer (QCSchema).

This package contains deep learning models and related scripts for RoseTTAFold

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

A pocket volume analyzer for use in protein modeling.