Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer
The data provided and described here give insight into the solution dynamics of the dimer of human EpCAM ectodomain (EpEX). As the starting point, crystal structure of EpEX non-covalent dimer was used (PDB ID 4MZV). The coordinates of solvent-embedded dimer were used to generate a topology file, whi...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-10-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340921006855 |
| _version_ | 1819027173106778112 |
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| author | Miha Pavšič |
| author_facet | Miha Pavšič |
| author_sort | Miha Pavšič |
| collection | DOAJ |
| description | The data provided and described here give insight into the solution dynamics of the dimer of human EpCAM ectodomain (EpEX). As the starting point, crystal structure of EpEX non-covalent dimer was used (PDB ID 4MZV). The coordinates of solvent-embedded dimer were used to generate a topology file, which was in turn used for all-atom molecular dynamics (MD) simulation run of 20 ns length using full-system periodic electrostatics at a constant temperature of 310 K and a constant pressure of 1 atm. The MD trajectory file (part of this dataset) contains 4000 frames corresponding to recording/sampling atom positions every 5 ps. The simulation run was then analyzed in terms of root mean square deviations (RMSD) of protein atoms, and non-covalent inter-subunit interactions. The MD trajectory and analyzed data enable—in contrast to the static crystal structure—detailed analysis of solution-like protein structural dynamics and support design of EpCAM-targetting binders and structure-based analysis of EpCAM interactome. |
| first_indexed | 2024-12-21T05:38:15Z |
| format | Article |
| id | doaj.art-d065af37d9644eafb10d752f3714c832 |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-21T05:38:15Z |
| publishDate | 2021-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-d065af37d9644eafb10d752f3714c8322022-12-21T19:14:20ZengElsevierData in Brief2352-34092021-10-0138107403Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimerMiha Pavšič0Faculty of Chemistry and Chemical Technology, Department of Chemistry and Biochemistry, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, SloveniaThe data provided and described here give insight into the solution dynamics of the dimer of human EpCAM ectodomain (EpEX). As the starting point, crystal structure of EpEX non-covalent dimer was used (PDB ID 4MZV). The coordinates of solvent-embedded dimer were used to generate a topology file, which was in turn used for all-atom molecular dynamics (MD) simulation run of 20 ns length using full-system periodic electrostatics at a constant temperature of 310 K and a constant pressure of 1 atm. The MD trajectory file (part of this dataset) contains 4000 frames corresponding to recording/sampling atom positions every 5 ps. The simulation run was then analyzed in terms of root mean square deviations (RMSD) of protein atoms, and non-covalent inter-subunit interactions. The MD trajectory and analyzed data enable—in contrast to the static crystal structure—detailed analysis of solution-like protein structural dynamics and support design of EpCAM-targetting binders and structure-based analysis of EpCAM interactome.http://www.sciencedirect.com/science/article/pii/S2352340921006855EpCATumor markerMolecular dynamics simulationStructureResidue-residue contact network |
| spellingShingle | Miha Pavšič Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer Data in Brief EpCA Tumor marker Molecular dynamics simulation Structure Residue-residue contact network |
| title | Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer |
| title_full | Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer |
| title_fullStr | Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer |
| title_full_unstemmed | Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer |
| title_short | Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer |
| title_sort | dataset and analysis of molecular dynamics simulation of epcam ectodomain dimer |
| topic | EpCA Tumor marker Molecular dynamics simulation Structure Residue-residue contact network |
| url | http://www.sciencedirect.com/science/article/pii/S2352340921006855 |
| work_keys_str_mv | AT mihapavsic datasetandanalysisofmoleculardynamicssimulationofepcamectodomaindimer |