3D Model Construction of SARS-CoV-2 Virus

  • Youssef Mesri (Creator)
  • Wael Bader (Creator)
  • Rabab Alomairy (Creator)
  • Hatem Ltaief (Creator)
  • David E. Keyes (Creator)
  • Youssef Mesri (Creator)
  • Wael Bader (Creator)
  • Rabab Alomairy (Creator)

    Dataset

    Description

    Description:
    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.
    Date made availableSep 6 2020
    PublisherKAUST Research Repository

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