PN 3

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

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1 to 10 of 1,091 Results

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...
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
EcoliPLE_DTC.tar.gz Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms" Gzip Archive - 148.3 GB - MD5: a091ecd2147a2fb685f9a64f169988c1
EcoliPLE_NSA.tar.gz Aug 11, 2026 - Supplementary Data to: "Disulfiram inhibits pyroptosis and apoptosis through multiple complementary mechanisms" Gzip Archive - 243.2 GB - MD5: 1a5f304a2c0c4d72d5fd672a5241491b

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...

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 -