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@BrooksResearchGroup-UM Brooks Group at the University of Michigan

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    18 repositories

    • ALF_CpHMD

      Public
      Automated CpHMD Simulation Pipeline based on ALF and Replica Exchange
      Rich Text Format
      •0•1•0•0•Updated Jan 20, 2025Jan 20, 2025

    • 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
      •
      MIT License
      •10•63•3•0•Updated Jan 20, 2025Jan 20, 2025

    • pyCHARMM-CHARMM-GPU-Benchmarks

      Public
      This repository provides the latest benchmarks for the CHARMM/pyCHARMM program on GPUs
      charmmgpu-performancepycharmm
      Rich Text Format
      •0•2•0•0•Updated Jan 6, 2025Jan 6, 2025

    • latent_space_paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

    • crimm

      Public
      Rich Text Format
      •
      GNU General Public License v3.0
      •1•5•9•0•Updated Oct 17, 2024Oct 17, 2024

    • seq_struct_func

      Public
      Example scripts for navigating protein sequence structure function space.
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Sep 19, 2024Sep 19, 2024

    • anc_acyl

      Public
      ReScript
      •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • FastMBAR

      Public
      A fast solver for large scale MBAR/UWHAM equations
      Python
      •
      MIT License
      •8•38•0•1•Updated Sep 4, 2024Sep 4, 2024

    • Ancestral_AT_paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 27, 2024Jun 27, 2024

    • 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
      •
      MIT License
      •5•8•1•0•Updated Aug 7, 2023Aug 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.
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 28, 2023Jul 28, 2023

    • ALF

      Public
      Adaptive landscape flattening scripts for use with CHARMM/pyCHARMM Multi-site lambda dynamics
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 28, 2023Jul 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
      Shell
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 28, 2023Jul 28, 2023

    • FASTDock

      Public
      FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook
      Rich Text Format
      •
      MIT License
      •1•18•1•0•Updated Jun 10, 2023Jun 10, 2023

    • PEVAE_Paper

      Public
      Deciphering protein evolution and fitness landscapes with latent space models
      Python
      •
      GNU General Public License v3.0
      •2•31•4•0•Updated Nov 2, 2021Nov 2, 2021

    • DirectCouplingAnalysis_PottsModel_Tensorflow

      Public
      A Tensorflow implementation of Direct Coupling Analysis using Potts model
      Python
      •2•10•0•0•Updated Oct 10, 2017Oct 10, 2017

    • CDOCKER

      Public
      Cuda
      •0•0•0•0•Updated Oct 7, 2016Oct 7, 2016

    • ML-Matching

      Public
      Machine Learning Approaching for Atom Typing.
      Python
      •0•2•0•0•Updated Aug 4, 2016Aug 4, 2016