PN 3-11

Biological Molecular Dynamics Simulations

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1 to 8 of 8 Results

Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB, a master virulence regulator in pathogenic Leptospira" Feb 10, 2026 Pluhackova, Kristyna, 2026, "Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB, a master virulence regulator in pathogenic Leptospira"", https://doi.org/10.18419/DARUS-5664, DaRUS, V1 Initial coordinate and simulation input files and a coordinate files of the final outputs as well as of the simulation trajectories (protein only) for all-atom MD simulations of LvrB performed using CHARMM36m/TIP4p in GROMACS2023. (pdb, xtc) Simulation data on phosphorylated aspartic acid (residue APP) with parameters generated by CHARMM-GUI are in...
Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" Feb 10, 2026 Korn, Viktoria Helena; Pluhackova, Kristyna, 2026, "Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"", https://doi.org/10.18419/DARUS-5682, DaRUS, V1 GROMACS simulation files, input and final structures for CHARMM36m MD simulations including our refined parameters for phosphorylated serine in 3 different protonation states. The directory charmm36-jul22mod.ff contains our refined parameters.
Supplementary data to "Roles of ligand, phosphorylation, and membrane in assembling human β2-adrenergic receptor-β-arrestin complexes" Feb 3, 2026 Pluhackova, Kristyna, 2026, "Supplementary data to "Roles of ligand, phosphorylation, and membrane in assembling human β2-adrenergic receptor-β-arrestin complexes"", https://doi.org/10.18419/DARUS-5513, DaRUS, V1 GROMACS simulation files, initial and final snapshots (all atoms) as well as simulation trajectories (proteins, ligands, membrane) of (i) beta-arrestin 2 (barr2) in inactive and active form interacting with a membrane with or without PIP2 lipids, (ii) beta2-adrenergic receptor activated by adrenaline and either phosphorylated on S355 and S356 or no...
Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF" Sep 9, 2025 Pluhackova, Kristyna, 2025, "Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"", https://doi.org/10.18419/DARUS-5324, DaRUS, V1 Simulation files, molecular structures and trajectories tetrameric GlpF wild type and M4C mutant. in the latter, 4 cysteine residues in the transmembrane helix bundle of GlpF, in detail C11, C28, C80, and C99 are replaced by glycines. The data underlays our publication on the role of those 4 cysteine residues for stability of membrane inserted tetr...
Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning Apr 16, 2025 Pluhackova, Kristyna; Pfaendner, Christian; Unger, Benjamin; Korn, Viktoria Helena, 2025, "Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning", https://doi.org/10.18419/DARUS-4134, DaRUS, V1 The simulation files, molecule topologies, and analysis workflows required to generate the results of our paper 'ART-SM: Boosting Fragment-Based Backmapping by Machine Learning' published in J. Chem. Theory Comput.. In details: simulations.tar.gz: Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top...
Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3' Nov 7, 2024 Korn, Viktoria Helena; Pluhackova, Kristyna, 2024, "Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'", https://doi.org/10.18419/DARUS-4474, DaRUS, V1 Simulation files, molecular structures and trajectories, and jupyter notebooks used for analysis underlaying our publication on membrane insertion of monomeric gasdermin D to E. coli polar lipid extract (PLE). In detail: charmm36-july2017.ff simulation directory for GROMACS 202X used and useful gromacs files (topologies and mdp files) jupyter noteb...
Supplementary Material for 'Entropic barrier of water permeation through single-file channels' Jun 30, 2023 Wachlmayr, Johann; Fläschner, Gotthold; Pluhackova, Kristyna; Sandtner, Walter; Siligan, Christine; Horner, Andreas, 2023, "Supplementary Material for 'Entropic barrier of water permeation through single-file channels'", https://doi.org/10.18419/DARUS-3390, DaRUS, V1 Facilitated water permeation through narrow biological channels is fundamental for all forms of life. This process involves dehydration of bulk water entering the single-file region and hydrogen bond formation with channel lining amino acid residues. Despite its significance in health and disease as well as for biotechnological applications the ene...
Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Mar 9, 2023 Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/DARUS-3373, DaRUS, V1 Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether...

Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB, a master virulence regulator in pathogenic Leptospira"

Feb 10, 2026

Pluhackova, Kristyna, 2026, "Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB, a master virulence regulator in pathogenic Leptospira"", https://doi.org/10.18419/DARUS-5664, DaRUS, V1

Initial coordinate and simulation input files and a coordinate files of the final outputs as well as of the simulation trajectories (protein only) for all-atom MD simulations of LvrB performed using CHARMM36m/TIP4p in GROMACS2023. (pdb, xtc) Simulation data on phosphorylated aspartic acid (residue APP) with parameters generated by CHARMM-GUI are in...

Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"

Feb 10, 2026

Korn, Viktoria Helena; Pluhackova, Kristyna, 2026, "Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"", https://doi.org/10.18419/DARUS-5682, DaRUS, V1

GROMACS simulation files, input and final structures for CHARMM36m MD simulations including our refined parameters for phosphorylated serine in 3 different protonation states. The directory charmm36-jul22mod.ff contains our refined parameters.

Supplementary data to "Roles of ligand, phosphorylation, and membrane in assembling human β2-adrenergic receptor-β-arrestin complexes"

Feb 3, 2026

Pluhackova, Kristyna, 2026, "Supplementary data to "Roles of ligand, phosphorylation, and membrane in assembling human β2-adrenergic receptor-β-arrestin complexes"", https://doi.org/10.18419/DARUS-5513, DaRUS, V1

GROMACS simulation files, initial and final snapshots (all atoms) as well as simulation trajectories (proteins, ligands, membrane) of (i) beta-arrestin 2 (barr2) in inactive and active form interacting with a membrane with or without PIP2 lipids, (ii) beta2-adrenergic receptor activated by adrenaline and either phosphorylated on S355 and S356 or no...

Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"

Sep 9, 2025

Pluhackova, Kristyna, 2025, "Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"", https://doi.org/10.18419/DARUS-5324, DaRUS, V1

Simulation files, molecular structures and trajectories tetrameric GlpF wild type and M4C mutant. in the latter, 4 cysteine residues in the transmembrane helix bundle of GlpF, in detail C11, C28, C80, and C99 are replaced by glycines. The data underlays our publication on the role of those 4 cysteine residues for stability of membrane inserted tetr...

Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning

Apr 16, 2025

Pluhackova, Kristyna; Pfaendner, Christian; Unger, Benjamin; Korn, Viktoria Helena, 2025, "Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning", https://doi.org/10.18419/DARUS-4134, DaRUS, V1

The simulation files, molecule topologies, and analysis workflows required to generate the results of our paper 'ART-SM: Boosting Fragment-Based Backmapping by Machine Learning' published in J. Chem. Theory Comput.. In details: simulations.tar.gz: Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top...

Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'

Nov 7, 2024

Korn, Viktoria Helena; Pluhackova, Kristyna, 2024, "Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'", https://doi.org/10.18419/DARUS-4474, DaRUS, V1

Simulation files, molecular structures and trajectories, and jupyter notebooks used for analysis underlaying our publication on membrane insertion of monomeric gasdermin D to E. coli polar lipid extract (PLE). In detail: charmm36-july2017.ff simulation directory for GROMACS 202X used and useful gromacs files (topologies and mdp files) jupyter noteb...

Supplementary Material for 'Entropic barrier of water permeation through single-file channels'

Jun 30, 2023

Wachlmayr, Johann; Fläschner, Gotthold; Pluhackova, Kristyna; Sandtner, Walter; Siligan, Christine; Horner, Andreas, 2023, "Supplementary Material for 'Entropic barrier of water permeation through single-file channels'", https://doi.org/10.18419/DARUS-3390, DaRUS, V1

Facilitated water permeation through narrow biological channels is fundamental for all forms of life. This process involves dehydration of bulk water entering the single-file region and hydrogen bond formation with channel lining amino acid residues. Despite its significance in health and disease as well as for biotechnological applications the ene...

Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Mar 9, 2023

Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/DARUS-3373, DaRUS, V1

Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether...

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