Repositories list

• awesome-protein-foundation-models

  Public
  A curated list of protein foundation models, protein language models (pLMs), and generative models for sequence, structure, and multimodal protein modeling.

  machine-learningawesomebioinformatics+ 13

  machine-learningawesomebioinformaticsdeep-learningprotein-structuretransformerscomputational-biologyproteinawesome-listrepresentation-learning+ 6

  MIT License

  •0•2•0•0•Updated Mar 20, 2026Mar 20, 2026

• inverse_folding_free_energies

  Public
  Code for the "Zero-shot protein stability prediction by inverse folding models: a free energy interpretation" paper.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Jan 16, 2026Jan 16, 2026

• HackathonEBM

  Public
  Jupyter Notebook

  •1•4•0•0•Updated Nov 24, 2025Nov 24, 2025

• poli

  Public
  A library of discrete objectives

  Python

  •

  MIT License

  •1•27•55•4•Updated Oct 5, 2025Oct 5, 2025

• poli-docs

  Public
  Documentation for poli and poli-baselines

  0•6•6•2•Updated Sep 28, 2025Sep 28, 2025

• poli-baselines

  Public
  A collection of objective functions and black box optimization algorithms related to proteins and small molecules

  Python

  •

  MIT License

  •6•9•16•4•Updated Mar 3, 2025Mar 3, 2025

• hdbo_benchmark

  Public
  Code for "A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences"

  Python

  •2•16•3•1•Updated Feb 24, 2025Feb 24, 2025

• BEND

  Public
  Benchmarking DNA Language Models on Biologically Meaningful Tasks

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •19•1•1•0•Updated Oct 31, 2024Oct 31, 2024

• poli-assets

  Public
  Assets and datasets for `poli` and `poli-baselines`

  0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

• protein_regression

  Public
  The codebase to replicate the analysis of "A systematic analysis of regression models for protein engineering" (2024).

  benchmarkmachine-learningcomputational-biology+ 1

  benchmarkmachine-learningcomputational-biologyuncertainty-quantification

  Jupyter Notebook

  •

  MIT License

  •2•5•0•0•Updated Jun 12, 2024Jun 12, 2024

• corel

  Public
  Python

  •

  MIT License

  •1•3•4•0•Updated Apr 12, 2024Apr 12, 2024

• stochman

  Public
  Algorithms for computations on random manifolds made easier

  pythonmachine-learningpytorch+ 2

  pythonmachine-learningpytorchmanifoldriemannian-geometry

  Python

  •

  Apache License 2.0

  •10•95•10•0•Updated Dec 4, 2023Dec 4, 2023

• .github

  Public
  0•1•0•0•Updated Aug 18, 2023Aug 18, 2023

• meaningful-protein-representations

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •7•110•4•0•Updated Mar 7, 2022Mar 7, 2022

• torchplot

  Public
  Plotting pytorch tensors made easy!

  Python

  •

  Apache License 2.0

  •1•15•0•0•Updated Jan 28, 2021Jan 28, 2021