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621 to 630 of 25,724 Results

training_inputs_and_labels_steadystate.zip Aug 18, 2026 - Step 3: Scaled-up Domain and Interactions of Heat Plumes ZIP Archive - 5.3 GB - MD5: 3c32d364b49033b6b791998eaeaded39 Data
training_inputs_and_labels_timeseries.zip Aug 18, 2026 - Step 3: Scaled-up Domain and Interactions of Heat Plumes ZIP Archive - 19.2 GB - MD5: 35a4517ccd3d554d7b7bd23c2cb9a650 Data
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...
general.zip Aug 14, 2026 - Step 1: Single Heat Plume ZIP Archive - 1.2 MB - MD5: 21a280212052c1dfd7c6fd1a5b697a08
test_labels_hidden.zip Aug 14, 2026 - Step 1: Single Heat Plume ZIP Archive - 377.4 MB - MD5: f07150ac613c2e263aa0883be1a4d9c1 Data Hidden prepared labels of test files. Access by request only.
training_inputs_and_labels_interimvelocities.zip Aug 14, 2026 - Step 1: Single Heat Plume ZIP Archive - 19.5 GB - MD5: 14b8891aaa540b550a24b733ffed291f Data

training_inputs_and_labels_steadystate.zip

Aug 18, 2026 - Step 3: Scaled-up Domain and Interactions of Heat Plumes

ZIP Archive - 5.3 GB -

Data

training_inputs_and_labels_timeseries.zip

Aug 18, 2026 - Step 3: Scaled-up Domain and Interactions of Heat Plumes

ZIP Archive - 19.2 GB -

Data

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...

general.zip

Aug 14, 2026 - Step 1: Single Heat Plume

ZIP Archive - 1.2 MB -

test_labels_hidden.zip

Aug 14, 2026 - Step 1: Single Heat Plume

ZIP Archive - 377.4 MB -

Data

Hidden prepared labels of test files. Access by request only.

training_inputs_and_labels_interimvelocities.zip

Aug 14, 2026 - Step 1: Single Heat Plume

ZIP Archive - 19.5 GB -

Data

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