Comparative analysis of non structural protein 1 of SARS-CoV2 with SARS-CoV1 and MERS-CoV: An in silico study

  1. Ankur Chaudhuri

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Abstract

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  1. Version published to 10.1016/j.molstruc.2021.130854
  2. Version published to 10.1101/2020.06.09.142570v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.09.142570: (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
    The pairwise sequence identity between COVID-19 nsp1 protein and each of the other HCoV nsp1 proteins (SERS-COV1 and MERS-COV) was calculated using the BLASTp (basic local alignment tool) [17].
    BLASTp
    suggested: (BLASTP, RRID:SCR_001010)
    To check the conservation pattern, multiple sequence alignment (MSA) of all of the nsp1 sequences was performed using the Clustal Omega programme of the European Bioinformatics Institute (EMBL-EBI) [18].
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    So, in silico modelling study was employed to predict the three dimensional structure of nsp1 of SARS-COV2 and MERS-COV by using the I-TASSER web server [20]
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    These two methods recognize ligand-binding templates from the BioLiP database [28] by sequence profile comparisons and binding-specific substructure.
    BioLiP
    suggested: None
    , Pymol [42], and also the plots were created using xmgrace [43].
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 24 and 22. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.06.09.142570v1 on bioRxiv