interface-gpu

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

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

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

Differentiable, Hardware Accelerated, Molecular Dynamics

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

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

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

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

Code for running RFdiffusion

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

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

A Euclidean diffusion model for structure-based drug design.

GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning. Official Implementation of PocketVina

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.

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

AutoDock for GPUs and other accelerators

[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

This package contains deep learning models and related scripts for RoseTTAFold

Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 oral]