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baker-laboratory

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  1. RoseTTAFold-All-Atom RoseTTAFold-All-Atom Public

    Python 819 143

  2. rf_diffusion_all_atom rf_diffusion_all_atom Public

    Public RFDiffusionAA repo

    Python 487 93

  3. PLACER PLACER Public

    PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

    Python 267 40

  4. CA_RFDiffusion CA_RFDiffusion Public

    Python 78 15

  5. NA-MPNN NA-MPNN Public

    Python 69 10

  6. Metallohydrolase_Enzyme_Design Metallohydrolase_Enzyme_Design Public

    Official GitHub repository for the manuscript entitled "Computational Design of Metallohydrolases" by Kim, Woodbury, & Ahern et al. published in Nature. This notebook contains (1) tutorials on how …

    Jupyter Notebook 29 5

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Showing 10 of 14 repositories
  • Metallohydrolase_Enzyme_Design Public

    Official GitHub repository for the manuscript entitled "Computational Design of Metallohydrolases" by Kim, Woodbury, & Ahern et al. published in Nature. This notebook contains (1) tutorials on how to use RFdiffusion2 for enzyme design, (2) a demo pipeline for metallohydrolase design, and (3) data, sequences, and design models from the manuscript.

    baker-laboratory/Metallohydrolase_Enzyme_Design's past year of commit activity
    Jupyter Notebook 29 MIT 5 2 0 Updated Sep 10, 2026
  • baker-lab-manuscripts Public

    Baker Lab manuscript review and formatting skill

    baker-laboratory/baker-lab-manuscripts's past year of commit activity
    Python 0 0 0 0 Updated Sep 2, 2026
  • baker-lab-figure Public

    IPD/Baker Lab scientific figure creation, revision, and audit skill

    baker-laboratory/baker-lab-figure's past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Sep 2, 2026
  • worms Public

    working version of the worms code that can be compiled as of 2026-02-13

    baker-laboratory/worms's past year of commit activity
    Python 1 1 0 0 Updated Aug 27, 2026
  • NA-MPNN Public
    baker-laboratory/NA-MPNN's past year of commit activity
    Python 69 10 2 0 Updated Jul 15, 2026
  • catcif_tools Public

    A set of tools making it easier to work with catted cif files

    baker-laboratory/catcif_tools's past year of commit activity
    Python 0 0 0 0 Updated Jul 7, 2026
  • TMB_pipeline Public

    This repository contains tutorials for running a fully deep learning–based pipeline for transmembrane β-barrel (TMB) design. It includes notebooks demonstrating how to run TMB_RFD2 for backbone generation and TMB_MPNN for sequence design, as well as steps for curating and filtering the distillation set used for training. Resources

    baker-laboratory/TMB_pipeline's past year of commit activity
    Python 2 0 0 0 Updated Jun 23, 2026
  • RoseTTAFold-All-Atom Public
    baker-laboratory/RoseTTAFold-All-Atom's past year of commit activity
    Python 819 143 108 (1 issue needs help) 4 Updated May 18, 2026
  • CA_RFDiffusion Public
    baker-laboratory/CA_RFDiffusion's past year of commit activity
    Python 78 MIT 15 9 1 Updated May 4, 2026
  • PLACER Public

    PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

    baker-laboratory/PLACER's past year of commit activity
    Python 267 40 8 1 Updated Nov 5, 2025
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