interface-cli

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)

Python3 translation of AutoDockTools

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

Message Passing Neural Networks for Molecule Property Prediction

Standalone charge assignment from Espaloma framework.

Parameter/topology editor and molecular simulator

A pocket volume analyzer for use in protein modeling.

Predicting protein-ligand binding sites using deep convolutional neural network

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]

This package contains deep learning models and related scripts for RoseTTAFold

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.

Calculation of interatomic interactions in molecular structures

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

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

PyRod - Tracing water molecules in molecular dynamics simulations

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

Source code for molecular graphics program UCSF ChimeraX