Message Passing Neural Networks for Molecule Property Prediction

Standalone charge assignment from Espaloma framework.

Parameter/topology editor and molecular simulator

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

Python3 translation of AutoDockTools

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

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

Predicting protein-ligand binding sites using deep convolutional neural network

A pocket volume analyzer for use in protein modeling.

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]

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.

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

Source code for molecular graphics program UCSF ChimeraX

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

PyRod - Tracing water molecules in molecular dynamics simulations

[Sci. Adv. 2026] The official repository of our paper "Steering Semi-flexible Molecular Diffusion Model for Structure-Based Drug Design with Reinforcement Learning"

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.