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    18 repositories

    • GrandFEP

      Public
      Alchemical Free Energy Calculations with Grand Canonical Ensemble
      pythonsimulationmonte-carlo
      pythonsimulationmonte-carlomolecular-dynamicsopenmmalchemyfree-energyion-channelfree-energy-perturbationgcmc
      Python
      •
      MIT License
      •0•12•0•0•Updated Apr 8, 2026Apr 8, 2026

    • pmx

      Public
      Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
      Python
      •
      GNU Lesser General Public License v3.0
      •74•174•26•6•Updated Mar 11, 2026Mar 11, 2026

    • pmx_tutorials_inputs

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • pka_reparam_2025

      Public
      data and ff params for: "Improving pKa prediction accuracy with reparametrized force fields and free energy calculations"
      Python
      •0•3•0•0•Updated Feb 17, 2026Feb 17, 2026

    • aquaporin_3_2025

      Public
      0•0•0•0•Updated Dec 23, 2025Dec 23, 2025

    • abcg2_evaluation

      Public
      0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • public_benchmark2025

      Public
      0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • Charge_Scaling_in_Potassium_Channel_Simulations_paper

      Public
      Force field and structure file used in Charge Scaling in Potassium Channel Simulations: Conductance, Ion Occupancy, Voltage Response, and Selectivity
      Jupyter Notebook
      •1•6•0•0•Updated Jul 28, 2025Jul 28, 2025

    • Initial_Structure_Modeling_RBFE_2025

      Public
      0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • Sfilter_Cylinder

      Public
      Potassium Channle Selectivity Filter Counting
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Jan 25, 2025Jan 25, 2025

    • pka_coupling_2024

      Public
      data for the paper on resolving pKa of coupled residues, JCC, 2024
      Jupyter Notebook
      •0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

    • pka_prediction_2023

      Public
      data for https://doi.org/10.1021/acs.jctc.3c00721
      0•0•0•0•Updated Oct 13, 2023Oct 13, 2023

    • KPerm

      Public
      Analysis of permeation cycles in MD simulations of potassium channels
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 3, 2023Aug 3, 2023

    • abs_dG_paper_ChemScience2021

      Public
      structures and data for https://doi.org/10.1039/D1SC03472C
      C++
      •3•9•1•0•Updated Sep 27, 2022Sep 27, 2022

    • active_learning_JCTC2022

      Public
      Fata from the alchemy+ML paper in JCTC 2022
      Jupyter Notebook
      •1•0•0•0•Updated Sep 22, 2022Sep 22, 2022

    • icolos_pmx_paper_2022

      Public
      2•6•1•0•Updated Sep 14, 2022Sep 14, 2022

    • rel_ddG_MerckDataSet_JCIM

      Public
      Relative free energy calculation data for the Merck protein-ligand set
      1•8•1•0•Updated Feb 22, 2022Feb 22, 2022

    • pmx-feedstock

      Public
      A conda-smithy repository for pmx.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 30, 2019May 30, 2019
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