CoV3D: a database of high resolution coronavirus protein structures

  1. Ragul Gowthaman
  2. Johnathan D Guest
  3. Rui Yin
  4. Jared Adolf-Bryfogle
  5. William R Schief
  6. Brian G Pierce

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Abstract

SARS-CoV-2, the etiologic agent of COVID-19, exemplifies the general threat to global health posed by coronaviruses. The urgent need for effective vaccines and therapies is leading to a rapid rise in the number of high resolution structures of SARS-CoV-2 proteins that collectively reveal a map of virus vulnerabilities. To assist structure-based design of vaccines and therapeutics against SARS-CoV-2 and other coronaviruses, we have developed CoV3D, a database and resource for coronavirus protein structures, which is updated on a weekly basis. CoV3D provides users with comprehensive sets of structures of coronavirus proteins and their complexes with antibodies, receptors, and small molecules. Integrated molecular viewers allow users to visualize structures of the spike glycoprotein, which is the major target of neutralizing antibodies and vaccine design efforts, as well as sets of spike-antibody complexes, spike sequence variability, and known polymorphisms. In order to aid structure-based design and analysis of the spike glycoprotein, CoV3D permits visualization and download of spike structures with modeled N-glycosylation at known glycan sites, and contains structure-based classification of spike conformations, generated by unsupervised clustering. CoV3D can serve the research community as a centralized reference and resource for spike and other coronavirus protein structures, and is available at: https://cov3d.ibbr.umd.edu.

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  1. Version published to 10.1093/nar/gkaa731
  2. Version published to 10.1101/2020.05.12.091983v3 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.05.12.091983: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequence polymorphism information was obtained by BLAST search using a reference SARS-CoV-2 spike glycoprotein sequence (QHD43416.1).
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    , betacoronavirus spike glycoprotein sequences were downloaded from NCBI Virus (13) and aligned with Clustal Omega (14) in SeaView (15).
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    SeaView
    suggested: (SeaView, RRID:SCR_015059)
    Sequence logos are generated dynamically for user-specified residue ranges using the command-line version of WebLogo (16).
    WebLogo
    suggested: (WEBLOGO, RRID:SCR_010236)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

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  4. Version published to 10.1101/2020.05.12.091983v2 on bioRxiv
  5. Version published to 10.1101/2020.05.12.091983v1 on bioRxiv