status-published

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

AutoDock Vina

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

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

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

Molsystem provides a general class for handling molecular and periodic systems

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

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

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

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

WebGL accelerated JavaScript molecular graphics library

A deep learning framework for molecular docking

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

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

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).

Molecular Processing Made Easy.

A pocket volume analyzer for use in protein modeling.