Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning

Improved antibody structure-based design using inverse folding

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation

The Rosetta Bio-macromolecule modeling package.

ColabFold on your local PC

Learning to design protein-protein interactions with enhanced generalization (ICLR24)

A Python script to map PDB ID + chain ID to UniProt ID.

AlphaFold-initiated replica exchange protein docking

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities.

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Implementation of Denoising Diffusion Probabilistic Model in Pytorch

Making Protein Design accessible to all via Google Colab!

Language Modeling with the H3 State Space Model

Making Protein folding accessible to all!

Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch

Code for the ProteinMPNN paper

Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

Official release of the ProGen models

A library for graph deep learning research

Implementation of E(n)-Transformer, which extends the ideas of Welling's E(n)-Equivariant Graph Neural Network to attention

An all-atom protein structure dataset for machine learning.