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@BrooksResearchGroup-UM

Brooks Group at the University of Michigan

This site represents software projects developed within and distributed by the research group of Charles L. Brooks III at the University of Michigan.

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  1. pyCHARMM-Workshop pyCHARMM-Workshop Public

    pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.

    Jupyter Notebook 61 10

  2. FastMBAR FastMBAR Public

    A fast solver for large scale MBAR/UWHAM equations

    Python 35 8

  3. PEVAE_Paper PEVAE_Paper Public

    Deciphering protein evolution and fitness landscapes with latent space models

    Python 30 2

  4. FASTDock FASTDock Public

    FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook

    Rich Text Format 19 1

  5. DirectCouplingAnalysis_PottsModel_Tensorflow DirectCouplingAnalysis_PottsModel_Tensorflow Public

    A Tensorflow implementation of Direct Coupling Analysis using Potts model

    Python 10 2

  6. MSLD-Workshop MSLD-Workshop Public

    Materials for five day workshop on using MSLD (including ALF and MSLD_py_prep) for drug discovery and protein engineering

    Rich Text Format 8 5

Repositories

Showing 10 of 15 repositories
  • seq_struct_func Public

    Example scripts for navigating protein sequence structure function space.

    BrooksResearchGroup-UM/seq_struct_func’s past year of commit activity
    Jupyter Notebook 3 MIT 0 0 0 Updated Sep 19, 2024
  • anc_acyl Public
    BrooksResearchGroup-UM/anc_acyl’s past year of commit activity
    ReScript 0 0 0 0 Updated Sep 11, 2024
  • FastMBAR Public

    A fast solver for large scale MBAR/UWHAM equations

    BrooksResearchGroup-UM/FastMBAR’s past year of commit activity
    Python 35 MIT 8 0 1 Updated Sep 4, 2024
  • crimm Public
    BrooksResearchGroup-UM/crimm’s past year of commit activity
    Rich Text Format 4 GPL-3.0 1 9 0 Updated Jul 31, 2024
  • Ancestral_AT_paper Public
    BrooksResearchGroup-UM/Ancestral_AT_paper’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jun 27, 2024
  • pyCHARMM-Workshop Public

    pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.

    BrooksResearchGroup-UM/pyCHARMM-Workshop’s past year of commit activity
    Jupyter Notebook 61 MIT 10 2 0 Updated Sep 12, 2023
  • MSLD-Workshop Public

    Materials for five day workshop on using MSLD (including ALF and MSLD_py_prep) for drug discovery and protein engineering

    BrooksResearchGroup-UM/MSLD-Workshop’s past year of commit activity
    Rich Text Format 8 MIT 5 1 0 Updated Aug 7, 2023
  • BLaDE Public

    BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics on graphical processor units.

    BrooksResearchGroup-UM/BLaDE’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Jul 28, 2023
  • ALF Public

    Adaptive landscape flattening scripts for use with CHARMM/pyCHARMM Multi-site lambda dynamics

    BrooksResearchGroup-UM/ALF’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Jul 28, 2023
  • msld-prep Public

    A collection of python scripts and procedures to enable the building of ligands for Multi-site lambda Dynamics simulations using CHARMM/pyCHARMM

    BrooksResearchGroup-UM/msld-prep’s past year of commit activity
    Shell 1 GPL-3.0 0 0 0 Updated Jul 28, 2023
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