Repositories list

• pmx

  Public
  Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

  Python

  •

  GNU Lesser General Public License v3.0

  •7878 forks•182182 stars•2626 issues•66 pull requests•Updated Jul 28, 2026Jul 28, 2026

• TREK2_updown

  Public
  Raw data and scripts

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 12, 2026May 12, 2026

• GrandFEP

  Public
  Alchemical Free Energy Calculations with Grand Canonical Ensemble

  pythonsimulationmonte-carlo+ 8

  pythonsimulationmonte-carlomolecular-dynamicsopenmmalchemyfree-energyion-channelfree-energy-perturbationgcmc+ 1

  Python

  •

  MIT License

  •11 fork•2020 stars•00 issues•00 pull requests•Updated May 2, 2026May 2, 2026

• pmx_tutorials_inputs

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•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

  •00 forks•33 stars•00 issues•00 pull requests•Updated Feb 17, 2026Feb 17, 2026

• aquaporin_3_2025

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Dec 23, 2025Dec 23, 2025

• abcg2_evaluation

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Oct 31, 2025Oct 31, 2025

• public_benchmark2025

  Public
  00 forks•00 stars•00 issues•00 pull requests•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

  •11 fork•66 stars•00 issues•00 pull requests•Updated Jul 28, 2025Jul 28, 2025

• Initial_Structure_Modeling_RBFE_2025

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 29, 2025Apr 29, 2025

• Sfilter_Cylinder

  Public
  Potassium Channle Selectivity Filter Counting

  Jupyter Notebook

  •

  MIT License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jan 25, 2025Jan 25, 2025

• pka_coupling_2024

  Public
  data for the paper on resolving pKa of coupled residues, JCC, 2024

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 13, 2024Mar 13, 2024

• pka_prediction_2023

  Public
  data for https://doi.org/10.1021/acs.jctc.3c00721

  00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 3, 2023Aug 3, 2023

• abs_dG_paper_ChemScience2021

  Public
  structures and data for https://doi.org/10.1039/D1SC03472C

  C++

  •33 forks•1010 stars•11 issue•00 pull requests•Updated Sep 27, 2022Sep 27, 2022

• active_learning_JCTC2022

  Public
  Fata from the alchemy+ML paper in JCTC 2022

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 22, 2022Sep 22, 2022

• icolos_pmx_paper_2022

  Public
  22 forks•77 stars•11 issue•00 pull requests•Updated Sep 14, 2022Sep 14, 2022

• rel_ddG_MerckDataSet_JCIM

  Public
  Relative free energy calculation data for the Merck protein-ligand set

  11 fork•88 stars•11 issue•00 pull requests•Updated Feb 22, 2022Feb 22, 2022

• pmx-feedstock

  Public
  A conda-smithy repository for pmx.

  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 30, 2019May 30, 2019