Repositories list

• hermes_experiments

  Public
  code, data and results of experiments shown in the HERMES paper

  Python

  •00 forks in StatPhysBio/hermes_experiments•00 stars in StatPhysBio/hermes_experiments•00 issues in StatPhysBio/hermes_experiments•00 pull requests in StatPhysBio/hermes_experiments•Updated Oct 31, 2026Oct 31, 2026

• hermes

  Public
  Python

  •

  MIT License

  •22 forks in StatPhysBio/hermes•1616 stars in StatPhysBio/hermes•00 issues in StatPhysBio/hermes•00 pull requests in StatPhysBio/hermes•Updated Sep 27, 2026Sep 27, 2026

• tcr_antigen_design

  Public
  Jupyter Notebook

  •00 forks in StatPhysBio/tcr_antigen_design•1414 stars in StatPhysBio/tcr_antigen_design•00 issues in StatPhysBio/tcr_antigen_design•00 pull requests in StatPhysBio/tcr_antigen_design•Updated Aug 26, 2026Aug 26, 2026

• pasc

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks in StatPhysBio/pasc•00 stars in StatPhysBio/pasc•00 issues in StatPhysBio/pasc•00 pull requests in StatPhysBio/pasc•Updated Apr 28, 2026Apr 28, 2026

• designimmune

  Public
  Studying information transmission in the adaptive immune response

  Jupyter Notebook

  •

  MIT License

  •00 forks in StatPhysBio/designimmune•11 star in StatPhysBio/designimmune•00 issues in StatPhysBio/designimmune•00 pull requests in StatPhysBio/designimmune•Updated Mar 24, 2026Mar 24, 2026

• foundry

  Public
  Central repository for biomolecular foundation models with shared trainers and pipeline components

  Python

  •

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

  •202202 forks in StatPhysBio/foundry•11 star in StatPhysBio/foundry•00 issues in StatPhysBio/foundry•00 pull requests in StatPhysBio/foundry•Updated Jan 23, 2026Jan 23, 2026

• hpacker

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks in StatPhysBio/hpacker•11 star in StatPhysBio/hpacker•00 issues in StatPhysBio/hpacker•00 pull requests in StatPhysBio/hpacker•Updated May 5, 2025May 5, 2025

• Holographic-VAE

  Public
  Python

  •

  MIT License

  •00 forks in StatPhysBio/Holographic-VAE•00 stars in StatPhysBio/Holographic-VAE•00 issues in StatPhysBio/Holographic-VAE•00 pull requests in StatPhysBio/Holographic-VAE•Updated May 5, 2025May 5, 2025

• biophysics

  Public
  Jupyter Notebook

  •22 forks in StatPhysBio/biophysics•22 stars in StatPhysBio/biophysics•00 issues in StatPhysBio/biophysics•00 pull requests in StatPhysBio/biophysics•Updated Apr 7, 2025Apr 7, 2025

• zernikegrams

  Public
  Stand-alone library for protein preprocessing

  Python

  •

  MIT License

  •00 forks in StatPhysBio/zernikegrams•22 stars in StatPhysBio/zernikegrams•11 issue in StatPhysBio/zernikegrams•00 pull requests in StatPhysBio/zernikegrams•Updated Feb 14, 2025Feb 14, 2025

• protein_biophysics

  Public
  Collection of biophysical tools for manipulating proteins (e.g. pyrosetta)

  Python

  •00 forks in StatPhysBio/protein_biophysics•00 stars in StatPhysBio/protein_biophysics•00 issues in StatPhysBio/protein_biophysics•00 pull requests in StatPhysBio/protein_biophysics•Updated Nov 5, 2024Nov 5, 2024

• protein_holography

  Public
  Code for holographic machine learning of proteins

  HTML

  •

  MIT License

  •44 forks in StatPhysBio/protein_holography•2525 stars in StatPhysBio/protein_holography•22 issues in StatPhysBio/protein_holography•22 pull requests in StatPhysBio/protein_holography•Updated Oct 29, 2024Oct 29, 2024

• dssp

  Public
  Application to assign secondary structure to proteins

  C++

  •

  BSD 2-Clause "Simplified" License

  •3434 forks in StatPhysBio/dssp•00 stars in StatPhysBio/dssp•00 issues in StatPhysBio/dssp•00 pull requests in StatPhysBio/dssp•Updated Oct 28, 2024Oct 28, 2024

• protein_holography-web

  Public
  Python

  •00 forks in StatPhysBio/protein_holography-web•55 stars in StatPhysBio/protein_holography-web•00 issues in StatPhysBio/protein_holography-web•00 pull requests in StatPhysBio/protein_holography-web•Updated Oct 2, 2024Oct 2, 2024

• ProteinMPNN-finetuning

  Public
  Code for the ProteinMPNN paper + fine-tuning functionalities

  Jupyter Notebook

  •

  MIT License

  •512512 forks in StatPhysBio/ProteinMPNN-finetuning•00 stars in StatPhysBio/ProteinMPNN-finetuning•00 issues in StatPhysBio/ProteinMPNN-finetuning•00 pull requests in StatPhysBio/ProteinMPNN-finetuning•Updated Aug 14, 2024Aug 14, 2024

• Working_memory

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks in StatPhysBio/Working_memory•11 star in StatPhysBio/Working_memory•00 issues in StatPhysBio/Working_memory•00 pull requests in StatPhysBio/Working_memory•Updated Dec 7, 2021Dec 7, 2021

• Tomoko

  Public
  Forward time simulator of genotypic evolution and fitness inference

  Julia

  •

  MIT License

  •00 forks in StatPhysBio/Tomoko•11 star in StatPhysBio/Tomoko•00 issues in StatPhysBio/Tomoko•00 pull requests in StatPhysBio/Tomoko•Updated Dec 1, 2021Dec 1, 2021

• HIVTreatmentOptimization

  Public
  Analysis of untreated patient sequences and viremia data for the purposes of optimizing passive-transfer bNAb therapy

  Mathematica

  •00 forks in StatPhysBio/HIVTreatmentOptimization•22 stars in StatPhysBio/HIVTreatmentOptimization•00 issues in StatPhysBio/HIVTreatmentOptimization•00 pull requests in StatPhysBio/HIVTreatmentOptimization•Updated Nov 24, 2021Nov 24, 2021

• EscapeSimulator

  Public
  Simulate the escape dynamics of HIV-1 against all your favorite antibody combinations

  Julia

  •

  MIT License

  •00 forks in StatPhysBio/EscapeSimulator•11 star in StatPhysBio/EscapeSimulator•00 issues in StatPhysBio/EscapeSimulator•00 pull requests in StatPhysBio/EscapeSimulator•Updated Nov 17, 2021Nov 17, 2021

• ImmuneMemoryDM

  Public
  analysis for Optimal evolutionary decision-making to store immune memory

  Jupyter Notebook

  •

  MIT License

  •00 forks in StatPhysBio/ImmuneMemoryDM•11 star in StatPhysBio/ImmuneMemoryDM•00 issues in StatPhysBio/ImmuneMemoryDM•00 pull requests in StatPhysBio/ImmuneMemoryDM•Updated May 10, 2021May 10, 2021

• covid-bcr

  Public
  Analysis of BCR repertoires from covid-19 infections

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks in StatPhysBio/covid-bcr•66 stars in StatPhysBio/covid-bcr•00 issues in StatPhysBio/covid-bcr•00 pull requests in StatPhysBio/covid-bcr•Updated Mar 19, 2021Mar 19, 2021