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

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.

[NeurIPS2025 Spotlight 🔥 ] Official implementation of "UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection"

A deep learning framework for molecular docking

This package contains deep learning models and related scripts for RoseTTAFold

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

Differentiable, Hardware Accelerated, Molecular Dynamics

Code for running RFdiffusion

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

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

PhoreGen: Pharmacophore-Oriented 3D Molecular Generation towards Efficient Feature-Customized Drug Discovery https://www.nature.com/articles/s43588-025-00850-5

A Euclidean diffusion model for structure-based drug design.

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

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

[PNAS 2025] Code of "Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design".

Code for the DISCO model: General Multimodal Protein Design Enables DNA-Encoding of Chemistry

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

AutoDock for GPUs and other accelerators

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Ligand Binding Site detection using Deep Learning