AutoDock Vina

Message Passing Neural Networks for Molecule Property Prediction

Standalone charge assignment from Espaloma framework.

Biomolecular simulation trajectory/data analysis.

Parameter/topology editor and molecular simulator

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

Python3 translation of AutoDockTools

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

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

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.

A deep learning framework for molecular docking

Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.

Calculation of interatomic interactions in molecular structures

Identification of Protein-Ligand Binding Sites using dipolar EPR data

Semiempirical Extended Tight-Binding Program Package

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

Prediction of binding residues for metal ions, nucleic acids, and small molecules.