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

AutoDock Vina

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"

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.

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

Molsystem provides a general class for handling molecular and periodic systems

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

WebGL accelerated JavaScript molecular graphics library

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

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

A Pharmacophore MultiToolkit designed to simplify and streamline the detection, generation, analysis, comparison, and application of pharmacophore models in drug-design strategies.

bedtools - the swiss army knife for genome arithmetic

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

Source code for molecular graphics program UCSF ChimeraX