Differentiable, Hardware Accelerated, Molecular Dynamics

AutoDock Vina

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

📐 Symmetry-corrected RMSD in Python

A Euclidean diffusion model for structure-based drug design.

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

Some useful RDKit functions

Parameter/topology editor and molecular simulator

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

Jupyter widget to interactively view molecular structures and trajectories

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

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

3D ligand-based pharmacophore modeling

bedtools - the swiss army knife for genome arithmetic

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

Application to assign secondary structure to proteins

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)