Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

  1. Weria Pezeshkian
  2. Fabian Grünewald
  3. Oleksandr Narykov
  4. Senbao Lu
  5. Valeria Arkhipova
  6. Alexey Solodovnikov
  7. Tsjerk A. Wassenaar
  8. Siewert J. Marrink
  9. Dmitry Korkin

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Abstract

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  1. Version published to 10.1016/j.str.2023.02.006
  2. Version published to 10.1101/2021.09.15.459697v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.09.15.459697: (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 top 10 models were then selected and the models of M homodimers were obtained using two symmetric docking approaches, SymDock and Galaxy 4-6.
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    We then placed the M-dimer model into the experimental EM density map of the ORF3a dimer (EMD-22139 11) using Phenix 15 and relied on the EM map to further refine the structure in ISOLDE 16, a package for UCSF Chimera X molecular visualization program 17.
    Phenix
    suggested: (Phenix, RRID:SCR_014224)
    All CG-MD simulations were performed using the GROMACS package (versions 2019) and the Martini 3 force field.
    GROMACS
    suggested: (GROMACS, RRID:SCR_014565)
    Results were plotted using Python 3.9 55 and Bokeh library 56
    Python
    suggested: (IPython, RRID:SCR_001658)
    A Sankey diagram of connected components was plotted in MATLAB 57 using visualization module of PisCES algorithm 58. 10.
    MATLAB
    suggested: (MATLAB, RRID:SCR_001622)
    We used the Mercator projection, which is a cylindrical projection that preserves local directions and shapes.
    Mercator
    suggested: (Mercator, RRID:SCR_014493)

    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 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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.09.15.459697v1 on bioRxiv