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

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

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

A deep learning framework for molecular docking

This package contains deep learning models and related scripts for RoseTTAFold

Differentiable, Hardware Accelerated, Molecular Dynamics

Code for running RFdiffusion

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

A Euclidean diffusion model for structure-based drug design.

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

Message Passing Neural Networks for Molecule Property Prediction

molfeat - the hub for all your molecular featurizers

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

IF-SitePred is a method for predicting ligand-binding sites on protein structures. It first generates an embedding for each residue of the protein using the ESM-IF1 (inverse folding) model, then performs point cloud clustering to identify binding site centers.

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

NequIP is a code for building E(3)-equivariant interatomic potentials

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