PN 3

SimTech EXC 2075 Project Network 3 "Data-integrated model reduction for particles and continua"

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1 to 10 of 1,102 Results

Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" May 11, 2026 - PN 3-11 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, V2 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.
charmm36-jul2022mod.ff.zip May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" ZIP Archive - 1.1 MB - MD5: e5e758a42a7a04a3af52bd2a3746f599 Ready-to-use CHARMM36m force field with our parameters for phosphorylated aminoacids
charmm_toppar_mod.zip May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" ZIP Archive - 1.4 MB - MD5: 10d788673880f41321b528dd43b8b042 Patched CHARMM36m force field files for CHARMM with our parameters
nmr_MD_sims.zip May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" ZIP Archive - 19.4 GB - MD5: bd30ce5c884d7dda4d9bb1b00d847840 DATA MD sims for calculating relaxation times and Excel sheet with all datapoints, including experimental values.
osmotic_experimental.zip May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" ZIP Archive - 53.9 KB - MD5: b871e4cc529a90ef9fc5fa93bf225b63 Measured osmotic concentration values for MPA and MAM
osmotic_mp2_ions_MD_sims.zip May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" ZIP Archive - 12.0 GB - MD5: e87671fc468f8473d2071eb6cbfab36a DATA osmotic pressure simulations of MP2 with sodium and guanidinium. Also simulations of MP2 with original charmm params scaled to -1 and MP2-1MAM with charge shifted from P to C
protein_simulations.zip May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching" ZIP Archive - 45.5 MB - MD5: 56a4af1e874bb6a8c90083dc1b152582 Anti-Sigma Factor Antagonist SpoIIAA simulations wild type and phosphorylated
Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira" Mar 20, 2026 - PN 3-11 Pluhackova, Kristyna; Hiller, Sebastian; Agustoni, Elia, 2026, "Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira"", https://doi.org/10.18419/DARUS-5664, DaRUS, V2 MD data (author K. Pluhackova): 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 parameter...
integrate_dotblot.ipynb Mar 20, 2026 - Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira" Jupyter Notebook - 2.1 MB - MD5: 5885976be7feaf3cc90987e5bc68e6c1 A script used to quantify dot intensities from an autophosphorylation assay.
YD_distance_pdb.tar.gz Mar 20, 2026 - Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira" Gzip Archive - 71.2 MB - MD5: 365384fb8ee779150cbd038def5a0015 Script used to statistically analyze domain structures of two-component systems, including pdb files.

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

May 11, 2026 - PN 3-11

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, V2

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.

charmm36-jul2022mod.ff.zip

May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"

ZIP Archive - 1.1 MB -

Ready-to-use CHARMM36m force field with our parameters for phosphorylated aminoacids

charmm_toppar_mod.zip

May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"

ZIP Archive - 1.4 MB -

Patched CHARMM36m force field files for CHARMM with our parameters

nmr_MD_sims.zip

May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"

ZIP Archive - 19.4 GB -

DATA

MD sims for calculating relaxation times and Excel sheet with all datapoints, including experimental values.

osmotic_experimental.zip

May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"

ZIP Archive - 53.9 KB -

Measured osmotic concentration values for MPA and MAM

osmotic_mp2_ions_MD_sims.zip

May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"

ZIP Archive - 12.0 GB -

DATA

osmotic pressure simulations of MP2 with sodium and guanidinium. Also simulations of MP2 with original charmm params scaled to -1 and MP2-1MAM with charge shifted from P to C

protein_simulations.zip

May 11, 2026 - Supplementary Material for "Refinement of CHARMM36m force field parameters for protein phosphorylation by force-matching"

ZIP Archive - 45.5 MB -

Anti-Sigma Factor Antagonist SpoIIAA simulations wild type and phosphorylated

Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira"

Mar 20, 2026 - PN 3-11

Pluhackova, Kristyna; Hiller, Sebastian; Agustoni, Elia, 2026, "Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira"", https://doi.org/10.18419/DARUS-5664, DaRUS, V2

MD data (author K. Pluhackova): 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 parameter...

integrate_dotblot.ipynb

Mar 20, 2026 - Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira"

Jupyter Notebook - 2.1 MB -

A script used to quantify dot intensities from an autophosphorylation assay.

YD_distance_pdb.tar.gz

Mar 20, 2026 - Supplementary Data to: "Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira"

Gzip Archive - 71.2 MB -

Script used to statistically analyze domain structures of two-component systems, including pdb files.

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