Differentiable, Hardware Accelerated, Molecular Dynamics

AutoDock Vina

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

Some useful RDKit functions

A Euclidean diffusion model for structure-based drug design.

📐 Symmetry-corrected RMSD in Python

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

bedtools - the swiss army knife for genome arithmetic

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

Application to assign secondary structure to proteins

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows

3D ligand-based pharmacophore modeling

A deep learning framework for molecular docking

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

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.

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

Jupyter widget to interactively view molecular structures and trajectories

Parameter/topology editor and molecular simulator