Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine

  1. Saba Ismail
  2. Sajjad Ahmad
  3. Syed Sikander Azam

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Abstract

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  1. Version published to 10.1016/j.molliq.2020.113612
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    SciScore for 10.1101/2020.04.05.026005: (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
    Antigenic epitopes were highlighted by VaxiJen 2.0 [45].
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    Allergenic epitopes were discarded through AllerTop 2.0 [46] and toxic potential of non-allergic epitopes was evaluated via ToxinPred [47].
    AllerTop
    suggested: (AllerTop, RRID:SCR_018496)
    Conservation across the world population of the final set of epitopes was done through IEDB epitope conservation analysis tool [49]. 2.2. Multi-Epitopes Peptide Vaccine Construct (MEPVC) Designing and Post Analysis: All filtered epitopes were linked together through AAY linkers [50] to design a multi-epitope peptide (MEP).
    Conservation
    suggested: (Conservation, RRID:SCR_016064)
    The physicochemical properties of designed MEPVC was predicted by ProtParam tool [51] of EXPASSY server.
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    The three dimensional (3D) structure of the MEPVC was modeled ab initio by 3Dpro of SCRATCH protein server [52].
    SCRATCH
    suggested: (SCRATCH, RRID:SCR_014291)
    SnapGene (https://www.snapgene.com/) was used to clone the optimized MEPVC cDNA into pET-28a (+) expression vector. 2.3. In Silico Immune Profiling of MEPVC: Immunogenic potential of the MEPVC was conducted in silico using C-ImmSim server [58,59].
    SnapGene
    suggested: (SnapGene, RRID:SCR_015052)
    The TLR3 receptor and MEPVC were used in a blind docking approach through an online PATCHDOCK server interface [65].
    PATCHDOCK
    suggested: (PatchDock, RRID:SCR_017589)

    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 page 24. 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.

  3. Version published to 10.1101/2020.04.05.026005v1 on bioRxiv