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Gray Lab

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  1. IgFold IgFold Public

    Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

    Python 319 60

  2. IgLM IgLM Public

    Generative Language Modeling for Antibody Design

    Python 120 22

  3. GeoDock GeoDock Public

    Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

    Python 83 13

  4. FLAb FLAb Public

    Fitness landscapes for antibodies

    Python 48 11

  5. AlphaRED AlphaRED Public

    AlphaFold-initiated replica exchange protein docking

    Python 41 6

  6. deepH3-distances-orientations deepH3-distances-orientations Public

    Python 34 9

Repositories

Showing 10 of 14 repositories
  • DFMDock Public

    DFMDock (Denoising Force Matching Dock), a diffusion model that unifies sampling and ranking within a single framework.

    Graylab/DFMDock’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Sep 29, 2024
  • MaskedProteinEnT Public
    Graylab/MaskedProteinEnT’s past year of commit activity
    Python 11 4 1 1 Updated Sep 28, 2024
  • AlphaRED Public

    AlphaFold-initiated replica exchange protein docking

    Graylab/AlphaRED’s past year of commit activity
    Python 41 MIT 6 3 3 Updated Aug 14, 2024
  • GeoDock Public

    Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

    Graylab/GeoDock’s past year of commit activity
    Python 83 MIT 13 5 0 Updated Jul 29, 2024
  • MPDock Public

    This repository contains the dataset of 29 transmembrane protein complexes of different rigidity along with their unbound protein structure. Additionally, there are scripts to submit relaxing and docking complexes given there unbound monomer structures.

    Graylab/MPDock’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Jul 5, 2024
  • FLAb Public

    Fitness landscapes for antibodies

    Graylab/FLAb’s past year of commit activity
    Python 48 11 4 0 Updated Apr 17, 2024
  • Implicit-Membrane-Energy-Function-Benchmark Public

    This is a set of scientific benchmark tests for evaluating membrane protein modeling energy functions. The test probe an energy function's ability to capture membrane protein orientation, stability, sequence, and structure. The methods are described in detail in the citations below.

    Graylab/Implicit-Membrane-Energy-Function-Benchmark’s past year of commit activity
    Scala 1 MIT 0 0 0 Updated Jan 19, 2024
  • IgLM Public

    Generative Language Modeling for Antibody Design

    Graylab/IgLM’s past year of commit activity
    Python 120 22 3 0 Updated Oct 12, 2023
  • IgFold Public

    Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

    Graylab/IgFold’s past year of commit activity
    Python 319 60 21 1 Updated Sep 3, 2023
  • CAPSIF Public

    CArbohydrate-Protein Site IdentiFier

    Graylab/CAPSIF’s past year of commit activity
    Jupyter Notebook 10 MIT 0 0 0 Updated Aug 22, 2023
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