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"

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

Parameter/topology editor and molecular simulator

Biomolecular simulation trajectory/data analysis.

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]

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

Message Passing Neural Networks for Molecule Property Prediction

Standalone charge assignment from Espaloma framework.

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.

Predicting protein-ligand binding sites using deep convolutional neural network