Scrutinizing the SARS-CoV-2 protein information for designing an effective vaccine encompassing both the T-cell and B-cell epitopes

  1. Neha Jain
  2. Uma Shankar
  3. Prativa Majee
  4. Amit Kumar

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 10.1016/j.meegid.2020.104648
  2. ScreenIT

    SciScore for 10.1101/2020.03.26.009209: (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
    Firstly, the antigenic proteins were analyzed by using NetMHCIIPan 3.2 server (http://www.cbs.dtu.dk/services/NetMHCIIpan/) [34].
    NetMHCIIPan
    suggested: None
    The structures of the SARS-CoV-2 proteins were constructed using I-TASSER (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) [43]and HTL and CTL epitopes were mapped and their structures were retrieved using PyMol tool.
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)
    The predicted epitopes were checked for their antigenicity using VaxiJen server, allergenicity by using AlgPred and toxicity by ToxinPred server. 9.
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    Solubility of the construct was calculated using SolPro tool available at SCRATCH protein predictor server (http://scratch.proteomics.ics.uci.edu/) [49].
    SolPro
    suggested: None
    SCRATCH
    suggested: (SCRATCH, RRID:SCR_014291)
    Vaccine construct structure prediction and validation: Secondary structure of the multi-epitope vaccine construct was predicted using SOPMA(https://npsa-prabi.ibcp.fr/cgibin/npsa_automat.pl?page=/NPSA/npsa_sopma.html) [50] and PSI-PRED (http://bioinf.cs.ucl.ac.uk/psipred/) server [51].
    http://bioinf.cs.ucl.ac.uk/psipred/
    suggested: (PSIPRED, RRID:SCR_010246)
    The structures were evaluated by constructing Ramachandran plot using RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) and the quality was assessed using ERRAT server (https://servicesn.mbi.ucla.edu/ERRAT/). 14.
    RAMPAGE
    suggested: (RAMPAGE, RRID:SCR_017590)
    Standard molecular dynamics of the vaccine construct: The refined modelled structure of the multi-epitope vaccine construct was further evaluated for its stability in the real environment by simulating it in a water sphere using NAMD-standard molecular dynamics tool (https://www.ks.uiuc.edu/Research/namd/) by using parallel processors.
    https://www.ks.uiuc.edu/Research/namd/
    suggested: (NAMD, RRID:SCR_014894)

    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 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 pages 32, 33 and 29. 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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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 10.1101/2020.03.26.009209v1 on bioRxiv