Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2

  1. Mahdi Ghorbani
  2. Bernard R. Brooks
  3. Jeffery B. Klauda

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Abstract

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  1. Version published to 10.1016/j.bpj.2021.02.047
  2. ScreenIT

    SciScore for 10.1101/2020.09.28.317206: (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
    RBD (residues of RBD away from RBM 330-440 and 509-520) and NTD (residues 13 to 310) Glycan-antibody overlap analysis: Antibodies that bind and neutralize spike protein are divided into three categories(39): antibodies that bind to the exposed part of RBD (RBM-binder), antibodies that bind to epitopes away from the RBM in RBD or RBD-binder and antibodies that bind to epitopes on NTD (NTD- binder).
    RBM-binder),
    suggested: None
    Three different antibodies were used in this study: B38 for RBM binder (PDB:7BZ5)(52), S309 for RBD binder (PDB:6WPT for open and PDB:6WPS for closed state)(53) and 4A8 antibody as NTD-binder (PDB:7C2L)(54).
    4A8
    suggested: None
    Software and Algorithms
    SentencesResources
    The temperature was maintained at 310 K using a Nosé- Hoover thermostat with a temperature coupling constant of 1 ps.(49) The production run lasted 1µs for each system (RBD-up and RBD-down) with a 2 fs timestep and the particle-mesh Ewald (PME)(50) for long range electrostatic interactions using GROMACS 2018.3 package.
    GROMACS
    suggested: (GROMACS, RRID:SCR_014565)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 6. 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.
    • 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

    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 10.1101/2020.09.28.317206v1 on bioRxiv