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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 333 62

  2. DL4Proteins-notebooks DL4Proteins-notebooks Public

    Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

    Jupyter Notebook 224 28

  3. IgLM IgLM Public

    Generative Language Modeling for Antibody Design

    Python 130 25

  4. GeoDock GeoDock Public

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

    Python 86 15

  5. FLAb FLAb Public

    Fitness landscapes for antibodies

    Python 54 11

  6. AlphaRED AlphaRED Public

    AlphaFold-initiated replica exchange protein docking

    Python 49 6

Repositories

Showing 10 of 15 repositories
  • DL4Proteins-notebooks Public

    Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

    Graylab/DL4Proteins-notebooks’s past year of commit activity
    Jupyter Notebook 224 28 0 0 Updated Dec 20, 2024
  • MaskedProteinEnT Public
    Graylab/MaskedProteinEnT’s past year of commit activity
    Python 11 4 0 2 Updated Dec 2, 2024
  • 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
    Python 28 MIT 4 1 0 Updated Nov 18, 2024
  • IgLM Public

    Generative Language Modeling for Antibody Design

    Graylab/IgLM’s past year of commit activity
    Python 130 25 4 0 Updated Oct 5, 2024
  • AlphaRED Public

    AlphaFold-initiated replica exchange protein docking

    Graylab/AlphaRED’s past year of commit activity
    Python 49 MIT 6 7 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 86 MIT 15 6 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 2 MIT 0 0 0 Updated Jul 5, 2024
  • FLAb Public

    Fitness landscapes for antibodies

    Graylab/FLAb’s past year of commit activity
    Python 54 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
  • 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 333 62 20 1 Updated Sep 3, 2023
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