interface-cli

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

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)

Parameter/topology editor and molecular simulator

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]

Predicting protein-ligand binding sites using deep convolutional neural network

A pocket volume analyzer for use in protein modeling.

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.

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.

Calculation of interatomic interactions in molecular structures

Source code for molecular graphics program UCSF ChimeraX

Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping