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    12 repositories

    • AlphaFold-IDP

      Public
      This repository provides with custom code and analysis scripts to generate structural ensembles of intrinsically disordered proteins by using AlphaFold generated residue distance maps as constraints in any prior-structural ensemble
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Dec 11, 2024Dec 11, 2024

    • AlphaFold-MetaInference-Tutorial

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Nov 11, 2024Nov 11, 2024

    • OpenMM-Plumed-MPI

      Public
      C++
      •1•3•0•0•Updated Oct 23, 2024Oct 23, 2024

    • PEABS-LC-MS

      Public
      tools for quantitative analysis of intact protein LC-MS for PEABS
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 19, 2024Feb 19, 2024

    • ab42-kinetic-ensemble

      Public
      Code for "A kinetic ensemble of the Alzheimer's Aβ peptide"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•5•0•0•Updated Jul 14, 2022Jul 14, 2022

    • sdab-entropy

      Public
      Comparison of the conformational entropy of designed and natural nanobodies
      Jupyter Notebook
      •0•3•0•0•Updated May 25, 2022May 25, 2022

    • ab42-g5-ensemble

      Public
      Code for "A small molecule stabilises the disordered native state of the Alzheimer’s Aβ peptide"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated May 24, 2022May 24, 2022

    • IAPP

      Public
      Shell
      •0•0•0•0•Updated May 4, 2022May 4, 2022

    • tau-microtubules

      Public
      Shell
      •0•0•0•0•Updated Mar 8, 2022Mar 8, 2022

    • Spike-OpeningTransitionEnsemble

      Public
      GROMACS-PLUMED input and analysis in manuscript "Determination of Intermediate State Structures in the Opening Pathway of SARS-CoV-2 Spike Using Cryo-Electron Microscopy"
      GNU General Public License v3.0
      •0•0•1•0•Updated Nov 25, 2020Nov 25, 2020

    • amyloid-beta_small_mol

      Public
      Mathematica
      •2•3•0•0•Updated Nov 1, 2020Nov 1, 2020

    • c-myc_small_mol

      Public
      These are the minimum input files required to rerun the simulations in Heller et al, Journal of Molecular Biology, 2017.
      1•0•0•0•Updated Apr 25, 2019Apr 25, 2019