Repositories list

• KcsA_string_method_FES

  Public
  Code to generate the data and figures of the ion channel KcsA string method simulation project.

  Jupyter Notebook

  •

  MIT License

  •1•1•0•0•Updated Apr 9, 2023Apr 9, 2023

• string-method-swarms-trajectories

  Public
  A python implementation of the string method with swarms of trajectories using GROMACS

  Python

  •

  MIT License

  •5•18•10•0•Updated Oct 19, 2022Oct 19, 2022

• electroporation_MD-CG_machine_learning

  Public
  In this project we study electroporation of membranes with realistic compositions using coarse-grained molecular dynamics simulations combined with machine learning and bayesian statistics.

  0•0•0•0•Updated Aug 23, 2022Aug 23, 2022

• InfleCS-free-energy-clustering-tutorial

  Public
  Python tutorial for estimating and clustering free energy landscapes with InfleCS.

  molecular-dynamicsfree-energyinflecs+ 1clustering

  Jupyter Notebook

  •

  MIT License

  •16•27•0•0•Updated May 6, 2022May 6, 2022

• allosteric-pathways

  Public
  Building and analyzing residue interaction networks with cofactors (includes tutorial).

  molecular-dynamicsnetwork-analysismolecular-dynamics-analysis+ 1currrent-flow

  Python

  •

  MIT License

  •8•17•1•0•Updated Mar 31, 2021Mar 31, 2021

• gpcr-string-method-2019

  Public
  molecular-dynamicsenhanced-samplingstring-method+ 2free-energy-calculationsgpcr

  Python

  •

  MIT License

  •3•1•0•0•Updated Feb 2, 2021Feb 2, 2021

• Informing_NMR_experiments_w_MD

  Public
  Code for: Informing NMR experiments with molecular dynamics simulations to characterize the dominant open state of KcsA. https://doi.org/10.1101/2020.12.14.422800

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Dec 18, 2020Dec 18, 2020

• demystifying

  Public
  machine-learningmolecular-dynamicsdeep-taylor-decomposition+ 1biomolecular-simulation

  Python

  •

  MIT License

  •8•19•9•0•Updated Jun 26, 2020Jun 26, 2020

• state-sampling

  Public
  Python code for finding single equlibirated states and analysis of GPCR data

  Python

  •

  MIT License

  •1•0•0•0•Updated Jun 23, 2020Jun 23, 2020

• GMM-free-energy-estimator_code-used-in-paper

  Public
  MATLAB

  •1•1•0•0•Updated Nov 29, 2017Nov 29, 2017