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dc.contributor.authorMesri, Youssef
dc.contributor.authorBader, Wael
dc.contributor.authorAlomairy, Rabab
dc.contributor.authorLtaief, Hatem
dc.contributor.authorKeyes, David E.
dc.date.accessioned2020-09-06T10:17:46Z
dc.date.available2020-09-06T10:17:46Z
dc.date.issued2020-09-06
dc.identifier.citationMesri, Y., Bader, W., Alomairy, R., Ltaief, H., & Keyes, D. E. (2020). 3D Model Construction of SARS-CoV-2 Virus [Data set]. KAUST Research Repository. https://doi.org/10.25781/KAUST-V2EF2
dc.identifier.doi10.25781/KAUST-V2EF2
dc.identifier.urihttp://hdl.handle.net/10754/664938
dc.descriptionDescription: The dataset contains SARS-COV-2 virus 3D geometry extracted from the Protein Data Bank (PDB) codenamed PDBID 6VXX available at (https://www.rcsb.org/structure/6VXX). In 3D model construction, we first generate a tetrahedral mesh of the volume surrounding the molecular structure of the Spike glycoprotein of the SARS-CoV-2 virus, a.k.a. the S protein from PDB. Codenamed PDBID 6VXX at the Protein Data Bank (PDB)2, the S protein has been generated with a 2.8Å resolution, i.e., 0.28nm. Once the mesh of the S protein has been constructed, We stitch several S proteins, approximately evenly distributed around the spheric geometry of the virus main body. Based on real geometrical description of the virus structure, we set the virus diameter to 140nm and attach 80 S proteins. We build a CAD model which represents the building block for the simulation pipeline. The CAD model is then triangulated to generate a 3D surface mesh of the overall SARS-COV-2 virus geometry. Software or equipment used to create the data: The mesh is generated using OxyGen Suite with third party tools: TetGen and VTK. OxyGen Suite is a collection of mesh generation, adaptation and deformation algorithms and tools that produces high quality static and dynamic simplex meshes.
dc.publisherKAUST Research Repository
dc.relation.isreferencedbyhttps://repository.kaust.edu.sa/bitstream/handle/10754/663637/hicma-rbf.pdf?sequence=4&isAllowed=y
dc.relation.urlhttps://github.com/ecrc/hicma
dc.rightsAttribution 3.0 United States
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/
dc.subject3D Mesh Deformation, Radial Basis Functions, Hydrodynamics, Low-Rank Matrix Approximation, High Performance Computing, COVID-19
dc.title3D Model Construction of SARS-CoV-2 Virus
dc.typeDataset
dc.contributor.departmentExtreme Computing Research Center
dc.contributor.departmentComputer, Electrical and Mathematical Sciences & Engineering Division
dc.relation.issupplementedbyDOI:10.25781/KAUST-PJVE2
refterms.dateFOA2020-09-06T10:17:47Z
kaust.request.doiyes
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Video]</i> <br/> Mesri, Y., Bader, W., Alomairy, R., Ltaief, H., &amp; Keyes, D. E. (2020). <i>Simulating the Unstructured Mesh Deformation of Moving SARS-CoV-2 Virus Bodies</i>. KAUST Research Repository. https://doi.org/10.25781/KAUST-PJVE2. DOI: <a href="https://doi.org/10.25781/KAUST-PJVE2" >10.25781/KAUST-PJVE2</a> Handle: <a href="http://hdl.handle.net/10754/665252" >10754/665252</a></a></li></ul>


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Attribution 3.0 United States
Except where otherwise noted, this item's license is described as Attribution 3.0 United States