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    15 repositories

    • DL4Proteins-notebooks

      Public
      Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
      deep-learningneural-networksconvolutional-neural-networksjupyter-notebookslanguage-modelprotein-designrna-designprotein-structure-predictiongraph-neural-networksdiffusion-models
      Jupyter Notebook
      •
      MIT License
      •37•293•0•1•Updated Jan 13, 2025Jan 13, 2025

    • FLAb

      Public
      Fitness landscapes for antibodies
      Python
      •
      MIT License
      •11•56•4•0•Updated Jan 13, 2025Jan 13, 2025

    • DFMDock

      Public
      DFMDock (Denoising Force Matching Dock), a diffusion model that unifies sampling and ranking within a single framework.
      Python
      •
      MIT License
      •4•28•1•0•Updated Jan 12, 2025Jan 12, 2025

    • MaskedProteinEnT

      Public
      Python
      •4•11•0•2•Updated Dec 2, 2024Dec 2, 2024

    • IgLM

      Public
      Generative Language Modeling for Antibody Design
      Python
      •
      Other
      •26•135•4•0•Updated Oct 5, 2024Oct 5, 2024

    • AlphaRED

      Public
      AlphaFold-initiated replica exchange protein docking
      Python
      •
      MIT License
      •11•65•7•3•Updated Aug 14, 2024Aug 14, 2024

    • GeoDock

      Public
      Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
      Python
      •
      MIT License
      •15•87•6•0•Updated Jul 29, 2024Jul 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.
      Python
      •
      MIT License
      •0•3•0•0•Updated Jul 5, 2024Jul 5, 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.
      Scala
      •
      MIT License
      •0•1•0•0•Updated Jan 19, 2024Jan 19, 2024

    • IgFold

      Public
      Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
      Python
      •
      Other
      •62•340•20•1•Updated Sep 3, 2023Sep 3, 2023

    • CAPSIF

      Public
      CArbohydrate-Protein Site IdentiFier
      Jupyter Notebook
      •
      MIT License
      •0•10•0•0•Updated Aug 22, 2023Aug 22, 2023

    • DeepSCAb

      Public
      Python
      •2•3•0•0•Updated Jul 6, 2022Jul 6, 2022

    • deepH3-distances-orientations

      Public
      Python
      •
      Other
      •9•34•5•0•Updated Nov 4, 2021Nov 4, 2021

    • dotfiles

      Public
      A collection of dotfiles for syncing multiple computers
      Python
      •1•0•0•0•Updated Mar 24, 2020Mar 24, 2020

    • graylab_config

      Public
      This repository serves as a storage space for lab-wide resources, such as shell aliases, useful scripts, etc. Please include a descriptive comment for everything you add to this repository.
      Shell
      •2•1•0•1•Updated Feb 25, 2013Feb 25, 2013