Popular GitHub Repositories for Protein Language Model

PocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets

Making Protein Modeling Accessible to All Biologists

Directed evolution of proteins in sequence space with gradients

Inference code for PoET: A generative model of protein families as sequences-of-sequences

SPECTRA: Spectral framework for evaluation of biomedical AI models

AutoML system for building trustworthy peptide bioactivity predictors

? Structure-aware adapter fine-tuning PLMs, with high training speed and impressive performance (Journal of Chemical Information and Modeling 2024).

Simple python interface for the OpenProtein.AI REST API.

Source code for Annotation-guided Protein Design with Multi-Level Domain Alignment. (KDD 2025)