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baker-laboratory

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

    Python 825 145

  2. rf_diffusion_all_atom rf_diffusion_all_atom Public

    Public RFDiffusionAA repo

    Python 492 94

  3. PLACER PLACER Public

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

    Python 269 42

  4. CA_RFDiffusion CA_RFDiffusion Public

    Python 80 16

  5. NA-MPNN NA-MPNN Public

    Python 71 11

  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 31 8

Repositories

Showing 10 of 16 repositories
  • CaGE Public
    baker-laboratory/CaGE's past year of commit activity
    Python 0 1 1 0 Updated Nov 2, 2026
  • 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 31 MIT 8 2 0 Updated Oct 30, 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 3 BSD-3-Clause 1 0 0 Updated Oct 28, 2026
  • NA-MPNN Public
    baker-laboratory/NA-MPNN's past year of commit activity
    Python 71 11 2 0 Updated Oct 8, 2026
  • ph_binder_paper Public

    Scripts for the pH binder paper

    baker-laboratory/ph_binder_paper's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 5, 2026
  • baker-lab-manuscripts Public

    Baker Lab manuscript review and formatting skill

    baker-laboratory/baker-lab-manuscripts's past year of commit activity
    Python 3 1 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 3 Apache-2.0 2 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
  • 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
  • RoseTTAFold-All-Atom Public
    baker-laboratory/RoseTTAFold-All-Atom's past year of commit activity
    Python 825 145 108 (1 issue needs help) 5 Updated May 18, 2026
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