Designing multi-epitope based peptide vaccine targeting spike protein SARS-CoV-2 B1.1.529 (Omicron) variant using computational approaches

  1. Meet Parmar
  2. Ritik Thumar
  3. Jigar Sheth
  4. Dhaval Patel

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  1. Version published to 10.1007/s11224-022-02027-6
  2. ScreenIT

    SciScore for 10.1101/2021.12.23.473990: (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

    Recombinant DNA
    SentencesResources
    The improved nucleotide was then cloned into the pET28a (+
    pET28a
    suggested: RRID:Addgene_114145)
    Software and Algorithms
    SentencesResources
    The GRAVY (Grand average of hydropathicity), half-life, sub-atomic weight, instability index, aliphatic record, and amino acid atomic composition of the protein sequence were computed through ProtParam (http://web.expasy.org/protparam/). 2. Prediction of B-cell linear and discontinuous epitopes: For identification of the linear B cell epitope areas in the antigen sequence, the ABCpred service was utilized.
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    The DiscoTope web server (Kringelum et al., 2012) was used to predict the surface area accessibility as well as amino acids that create discontinuous B-cell epitopes as identified through X-ray crystallography of antigen/antibody protein structures. 3.
    DiscoTope
    suggested: (DiscoTope, RRID:SCR_018530)
    To check the sequence homology of the MESV construct with human proteome, the MESV sequence was submitted for BLAST sequence homology tool.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    The homology model of MESV was constructed using I-TASSER (https://zhanggroup.org/I-TASSER/) webserver.
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    +) vector prototype using the SnapGene 4.2 tool. 11.
    SnapGene
    suggested: (SnapGene, RRID:SCR_015052)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 27. 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.

    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.

  3. Version published to 10.1101/2021.12.23.473990 on bioRxiv