Stars
Finetuning ProGen2 protein language model for generation of protein sequences from selected protein families.
Sequence-Structure-Surface Model for Protein Fitness Prediction (S3F)
This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.
FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models
MMseqs2: ultra fast and sensitive search and clustering suite
Biological foundation modeling from molecular to genome scale
Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
Official repository for the ProteinGym benchmarks
A trainable PyTorch reproduction of AlphaFold 3.
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and …
Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)
Public RFDiffusionAA repo
Implementation of Alphafold 3 from Google Deepmind in Pytorch
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
Awesome Protein Representation Learning
NeurIPS 2022, Revisiting Heterophily For Graph Neural Networks, official PyTorch implementation for Adaptive Channel Mixing (ACM) GNN framework
Implementation of the Paper: "Parameterized Hypercomplex Graph Neural Networks for Graph Classification" by Tuan Le, Marco Bertolini, Frank Noé and Djork-Arné Clevert