A ‘deep dive’ into the SARS-Cov-2 polymerase assembly: identifying novel allosteric sites and analyzing the hydrogen bond networks and correlated dynamics

  1. Khaled Barakat
  2. Marawan Ahmed
  3. Yasser Tabana
  4. Minwoo Ha

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1080/07391102.2021.1930162
  2. ScreenIT

    SciScore for 10.1101/2020.06.02.130849: (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
    For selecting the best templates to incorporate the missing residues, sequence alignments were performed in BLASTP suite using BLOSUM62 algorithm.
    BLASTP
    suggested: (BLASTP, RRID:SCR_001010)
    Several homology models were built using I-TASSER, Modeller Suite and SWISS-MODEL.
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    Clustering Analysis Protocol: To analyze the conformational dynamics of the bound nucleotides and to extract their dominant mode(s) of binding within the active site, we carried out RMSD conformational clustering on the whole MD trajectories.
    Clustering Analysis Protocol
    suggested: None
    To do that, we used accelerated MD simulations (AMDS) module as implemented in AMBER, which applied a boosting potential with a positive value (ΔV(r)) when the potential energy falls below a certain energy threshold39.
    AMBER
    suggested: (AMBER, RRID:SCR_016151)

    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.
    • 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.

  3. Version published to 10.1101/2020.06.02.130849v1 on bioRxiv