Code for the ProteinMPNN paper

Hardware go brrr bounded context suffix array construction algorithm

Multi-modal Molecule Structure-text Model for Text-based Editing and Retrieval, Nat Mach Intell 2023 (https://www.nature.com/articles/s42256-023-00759-6)

Diffusion models of protein structure; trigonometry and attention are all you need!

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

Cloud-based molecular simulations for everyone

End-to-end light-sheet image analysis for mouse brains, with DL training data generated in VR

B-field implementation in Rust

predicting peptide-protein interactions

Topological transformer for protein-ligand complex interaction prediction.

PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data

Generative Models for Graph-Based Protein Design

A machine learned Molecular Mechanics force field with integration into GROMACS and OpenMM

Improved antibody structure-based design using inverse folding

Code & data for "Protein Language Models Expose Viral Mimicry and Immune Escape"

An interoperable Python framework for biomolecular simulation.

Deep functional residue identification

Code for ICLR 2024 (Spotlight) paper "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"

Fast protein backbone generation with SE(3) flow matching.

Code for ColabDock paper

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

Open source implementation of AlphaFold3

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

Chai-1, SOTA model for biomolecular structure prediction

User friendly and accurate binder design pipeline

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

ATOM3D: tasks on molecules in three dimensions