PN 3

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

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1 to 10 of 1,130 Results

Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects" Aug 17, 2026 - PN 3-11 Pluhackova, Kristyna; Pfaendner, Christian; Unger, Benjamin; Paul, Thilo, 2026, "Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects"", https://doi.org/10.18419/DARUS-5853, DaRUS, V1 Simulation parameter files, protein pdb files for crystal structures and final simulation snapshots, Python scripts for FlexE and SphereGrinder, and Jupyter Notebooks to recreate our analyses and publication figures of the paper "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations an...
final_snapshots_and_starting_structures.tar.gz Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects" Gzip Archive - 18.6 MB - MD5: e8d2876bab653f231679c71d43433d47 Final snapshots and starting structures (PDB) for all conducted simulations. All structures are preprocessed, for example, to have the same atom numbering.
force_fields_and_mdp_files.tar.gz Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects" Gzip Archive - 1.2 MB - MD5: ab47a35e970fecdbccc559c08ab21454 amber19sb.ff - suitable also for GROMACS versions older than 2025, through explicit definition of different Calpha XC0, XC1 etc atom types; charmm36-jul22.ff; mdp_files - consecutively numbered for all 4 simulations setups: A19sb, C36m, C36mPs3p, C36mPs4p
python_scripts_flexe_spheregrinder_qcs.tar.gz Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects" Gzip Archive - 13.3 KB - MD5: b8af9e4b992d0285111cbc357cc75256 Implementation of FlexE and SphereGrinder; Modified getQCS.py script to enable running multiple instances of QCS in parallel
score_values_and_jupyter_notebooks.tar-1.gz Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects" Gzip Archive - 9.9 MB - MD5: 5fbd6b71a8b16f2b0247afa92b34722d Score values of final snapshots for simulation setups C36m, C36mPs3P, C36mPs4P, and A19sb as json files. Assessed scores are RMSD, TM-score, GDT, lDDT, SphereGrinder, CAD, QCS, FlexE, and MolProbity; GDT scores for snapshots over the trajectory (10ns apart) for simulation setups C36m, C36mPs3P, C36mPs4P, and A19sb. Jupyter notebooks for all relevan...
Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms" Aug 11, 2026 - PN 3-11 Pluhackova, Kristyna, 2026, "Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms"", https://doi.org/10.18419/DARUS-5538, DaRUS, V1 All-atom molecular dynamics simulations of disulfiram binding to caspase-1 as well as interactions of disulfiram (DSF), diethyldithiocarbamate (DTC), necrosulfonamide (NSA), and dimethylfumarate (DMF) with the E. Coli PLE membrane.
caspase-1_DSF.tar.gz Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms" Gzip Archive - 2.9 GB - MD5: 16932fc9a4e0162be13e563c7558a32c
caspase-1.tar.gz Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms" Gzip Archive - 2.8 GB - MD5: 20ee2213e80c8a6da30baeeeed5ee83c
EcoliPLE_DMF.tar.gz Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms" Gzip Archive - 107.1 GB - MD5: c9faf20550d9cf82264af29f33b9b652
EcoliPLE_DSF.tar.gz Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms" Gzip Archive - 192.6 GB - MD5: 1fc0888e66664c5c5feea9d468488007

Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects"

Aug 17, 2026 - PN 3-11

Pluhackova, Kristyna; Pfaendner, Christian; Unger, Benjamin; Paul, Thilo, 2026, "Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects"", https://doi.org/10.18419/DARUS-5853, DaRUS, V1

Simulation parameter files, protein pdb files for crystal structures and final simulation snapshots, Python scripts for FlexE and SphereGrinder, and Jupyter Notebooks to recreate our analyses and publication figures of the paper "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations an...

final_snapshots_and_starting_structures.tar.gz

Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects"

Gzip Archive - 18.6 MB -

Final snapshots and starting structures (PDB) for all conducted simulations. All structures are preprocessed, for example, to have the same atom numbering.

force_fields_and_mdp_files.tar.gz

Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects"

Gzip Archive - 1.2 MB -

amber19sb.ff - suitable also for GROMACS versions older than 2025, through explicit definition of different Calpha XC0, XC1 etc atom types; charmm36-jul22.ff; mdp_files - consecutively numbered for all 4 simulations setups: A19sb, C36m, C36mPs3p, C36mPs4p

python_scripts_flexe_spheregrinder_qcs.tar.gz

Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects"

Gzip Archive - 13.3 KB -

Implementation of FlexE and SphereGrinder; Modified getQCS.py script to enable running multiple instances of QCS in parallel

score_values_and_jupyter_notebooks.tar-1.gz

Aug 17, 2026 - Supplementary Material for "Which Metrics Best Capture Protein Structural Change in Molecular Dynamics Simulations? Evaluating Score Combinations and Force Field Effects"

Gzip Archive - 9.9 MB -

Score values of final snapshots for simulation setups C36m, C36mPs3P, C36mPs4P, and A19sb as json files. Assessed scores are RMSD, TM-score, GDT, lDDT, SphereGrinder, CAD, QCS, FlexE, and MolProbity; GDT scores for snapshots over the trajectory (10ns apart) for simulation setups C36m, C36mPs3P, C36mPs4P, and A19sb. Jupyter notebooks for all relevan...

Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms"

Aug 11, 2026 - PN 3-11

Pluhackova, Kristyna, 2026, "Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms"", https://doi.org/10.18419/DARUS-5538, DaRUS, V1

All-atom molecular dynamics simulations of disulfiram binding to caspase-1 as well as interactions of disulfiram (DSF), diethyldithiocarbamate (DTC), necrosulfonamide (NSA), and dimethylfumarate (DMF) with the E. Coli PLE membrane.

caspase-1_DSF.tar.gz

Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms"

Gzip Archive - 2.9 GB -

caspase-1.tar.gz

Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms"

Gzip Archive - 2.8 GB -

EcoliPLE_DMF.tar.gz

Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms"

Gzip Archive - 107.1 GB -

EcoliPLE_DSF.tar.gz

Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms"

Gzip Archive - 192.6 GB -

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