Revealing the Threat of Emerging SARS-CoV-2 Mutations to Antibody Therapies

  1. Jiahui Chen
  2. Kaifu Gao
  3. Rui Wang
  4. Guo-Wei Wei

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Abstract

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  1. Version published to 10.1016/j.jmb.2021.167155
  2. ScreenIT

    SciScore for 10.1101/2021.04.12.439473: (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

    Antibodies
    SentencesResources
    Additionally, a bipartition graph is introduced to describe the antibody and antigen in PPIs.
    antigen in PPIs.
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    The SKEMPI 2.0 is an updated version of the SKEMPI database, which contains new mutations and data from other three databases: AB-Bind [39], PROXiMATE [40], and dbMPIKT [41].
    AB-Bind
    suggested: None
    Software and Algorithms
    SentencesResources
    We take the first complete SARS-CoV-2 genome from the GenBank (NC_045512.2) as the reference genome [35], and the multiple sequence alignment is applied by the Clustal Omega [36, 37] with default parameters, which results in 27,530 single nucleotide polymorphism profiles.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    The implemented GBDT is a function from the scikit-learn package (version 0.22.2.post1) [49].
    scikit-learn
    suggested: (scikit-learn, RRID:SCR_002577)

    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.

    About SciScore

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  3. Version published to 10.1101/2021.04.12.439473v1 on bioRxiv