In silico Design and Characterization of Multi-epitopes Vaccine for SARS-CoV2 from Its Spike Protein

  1. Gunderao H. Kathwate

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 10.1007/s10989-021-10348-z
  2. Version published to 10.1101/2020.06.03.131755v3 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.03.131755: (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
    Selection of protein for epitope prediction: Complete Spike protein sequence (P0DTC2) of SARS-CoV2 was downloaded in fasta format from UniProt protein database.
    UniProt
    suggested: (UniProtKB, RRID:SCR_004426)
    Antigenicity of epitopes was analyzed by online server VaxiJen v2.0 (http://www.ddg-harmfac.net/vaxijen/VaxiJen/VaxiJen.html).
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    AllerTop v2.0 and AllergenFP were two online tools utilized for the prediction of allergenicity of chimeric protein.
    AllerTop
    suggested: (AllerTop, RRID:SCR_018496)
    PROSO II server works on an approach of classifier which utilizes difference between TargetDB and PDB and insoluble proteins of TargetDB.
    TargetDB
    suggested: None
    PSIPRED 3.2 attains average Q3 score of 81.6% obtained using very stringent cross approval strategies to assess its performance.
    PSIPRED
    suggested: (PSIPRED, RRID:SCR_010246)
    Tertiary structure of multi-epitopes chimeric vaccine candidate was built using I TASSER online server (https://zhanglab.ccmb.med.umich.edu/I-TASSER/).
    https://zhanglab.ccmb.med.umich.edu/I-TASSER/
    suggested: (I-TASSER, RRID:SCR_014627)
    Structure refined by Galaxy server of best quality in accordance with community-wide CASP10 experiments(58).
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    ProSA-web (https://prosa.services.came.sbg.ac.at/prosa.php), The ERRAT server (http://services.mbi.ucla.edu/ERRAT/) and RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) web servers were utilized for 3D structure validation obtained after galaxy server refinement(59)
    RAMPAGE
    suggested: (RAMPAGE, RRID:SCR_017590)

    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: 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.

    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 10.1101/2020.06.03.131755v2 on bioRxiv
  5. Version published to 10.1101/2020.06.03.131755v1 on bioRxiv