Molecular Dynamics Simulation Data for "Polyamine dysregulation causes resistance to sodium channel–targeting antiseizure medications"

Zenodo (CERN European Organization for Nuclear Research)

Abstract

Repository structure Molecular dynamics analysis data for the CBZ (carbamazepine) and OXC (oxcarbazepine)simulations, plus the GROMACS topologies used to run them. ./├── CBZ_analysis/ distance and density data for CBZ simulations├── OXC_analysis/ distance and density data for OXC simulations└── GROMACS_Topologies/ .tpr run inputs and .itp topologies CBZ_analysis / OXC_analysis Each folder holds data for across three conditions: the drugalone, and the drug co-simulated with N1-acetyl-spermidine or N1-acetyl-spermine. Filename prefix identifies the simulation condition: [CBZ] / [OXC] — drug alone [CBZ+NSD] / [OXC+NSD] — drug co-simulated with NSD (residue name for N1-acetyl-spermidine) [CBZ+NSN] / [OXC+NSN] — drug co-simulated with NSN (residue name for N1-acetyl-spermine) [NSD] / [NSN] — NSD or NSN alone, no drug present .xvg files — dist_BindingSite [_Top|_Bottom].xvgMinimum-distance time series between the drug and binding site (BIG, F4, or F3)._Top / _Bottom distinguish the two channel copies in simulations that containtwo copies of the protein; no suffix means a single-channel simulation. .dx files — WithRadii_ [(+other)].dxVolumetric density map of co-simulated with (+other) or alone (e.g. WithRadii_NSD(+CBZ).dxis the NSD co-simulated with CBZ ). GROMACS_Topologies .tpr run input files (one per condition, named the same way as the prefixesabove) and the .itp molecule topologies (CBZ, NSD, NSN, OXC)they reference.

Authors 3

1. Alessia Piergentili

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

2. Simone Albani

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

3. Giulia Rossetti Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University