AutoDock Vina

Differentiable, Hardware Accelerated, Molecular Dynamics

bedtools - the swiss army knife for genome arithmetic

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

Some useful RDKit functions

A deep learning framework for molecular docking

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

Code for running RFdiffusion

A tool for retrosynthetic planning

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

Python interface of cpptraj

Molsystem provides a general class for handling molecular and periodic systems

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

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.

📐 Symmetry-corrected RMSD in Python

A Euclidean diffusion model for structure-based drug design.

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

Python3 translation of AutoDockTools