status-published

AutoDock Vina

End-To-End Molecular Dynamics (MD) Engine using PyTorch

A Molecular Topography MultiToolkit designed to simplify and streamline the detection, analysis, and characterization of protein pockets, cavities, channels, and binding sites.

Differentiable, Hardware Accelerated, Molecular Dynamics

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

Molsystem provides a general class for handling molecular and periodic systems

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)

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

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

OpenMM is a toolkit for molecular simulation using high performance GPU code.

WebGL accelerated JavaScript molecular graphics library

A project (and object) for storing, manipulating, and converting molecular mechanics data.

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

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Biomolecular simulation trajectory/data analysis.

Parameter/topology editor and molecular simulator