1. Zahra Yazdani
  2. Alireza Rafiei
  3. Mohammadreza Yazdani
  4. Reza Valadan

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  1. Version published to 10.2147/idr.s264573
  2. ScreenIT

    SciScore for 10.1101/2020.04.20.051557: (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
    2.1 Protein sequence retrieval: The protein sequences of spike glycoprotein (accession number of QIC53213.1), nucleocapsid phosphoprotein (QHU79211.1), membrane glycoprotein (QIC53207.1) and envelope protein (QIC53215.1) were driven using NCBI (https://www.ncbi.nlm.nih.gov/) databases and saved in FASTA format for subsequent analysis.
    https://www.ncbi.nlm.nih.gov/
    suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)
    2.5 Evaluation of antigenicity: Antigencity of epitopes was assessed by ANTIGENpro (http://scratch.proteomics.ics.uci.edu/) and VaxiJen v2.0 (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) servers.
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    After designing the vaccine, Several physicochemical parameters including molecular weight, theoretical isoelectric point (pI), total number of positive and negative residues, extinction coefficient, Instability index, half-life, aliphatic index, and grand average hydropathy (GRAVY) were computed using Expasy’s ProtParam at http://us.expasy.org/tools/protparam.html [61].
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    2.8 Tertiary structure development: The 3-D modeling of designed construct was predicted using the I-TASSER software (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) [61].
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    The RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php), and ERRAT (http://services.mbi.ucla.edu/ERRAT/) servers were used to validate the refined 3D structures obtained from Galaxy Refine web service.
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    PyMOL is an open-source that widely used for bimolecular function[65].
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    The MODELLER program and the Jmol viewer allow the prediction and visualization of immunoepitopes in a given protein sequence or structure.
    MODELLER
    suggested: (MODELLER, RRID:SCR_008395)
    Next, protein-protein docking of the vaccine structure (as ligand) and each TLR (as receptor) was performed by CLUSPRO 2.0 online server (cluspro.bu.edu/login.php).
    CLUSPRO
    suggested: (ClusPro, RRID:SCR_018248)

    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 pages 32, 35 and 31. 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.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • 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 10.1101/2020.04.20.051557v1 on bioRxiv