Parameter/topology editor and molecular simulator

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

Python3 translation of AutoDockTools

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

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

Message Passing Neural Networks for Molecule Property Prediction

Standalone charge assignment from Espaloma framework.

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

Calculation of interatomic interactions in molecular structures

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.

A pocket volume analyzer for use in protein modeling.

Predicting protein-ligand binding sites using deep convolutional neural network

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]

RXNMapper: Unsupervised attention-guided atom-mapping. Code complementing our Science Advances publication on "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions" (https://advances.sciencemag.org/content/7/15/eabe4166).

Adding hydrogens to molecular models

Experiments with expanded ensembles to explore chemical space

A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening