1. SciScore for 10.1101/2021.09.13.460130: (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
    PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) [24], SNAP2 (https://rostlab.org/services/snap2web/) [25],
    PolyPhen-2
    suggested: None
    http://genetics.bwh.harvard.edu/pph2/
    suggested: (PolyPhen: Polymorphism Phenotyping, RRID:SCR_013189)
    Mutation Assessor (http://mutationassessor.org/r3/) [26, 27], and Protein Analysis Through Evolutionary Relationships (PANTHER) coding SNP (cSNP) (http://www.pantherdb.org/tools/csnpScoreForm.jsp) [28] tools were used for the first analysis to determine the effects of the missense SNPs.
    PANTHER
    suggested: (PANTHER, RRID:SCR_004869)
    http://www.pantherdb.org/tools/csnpScoreForm.jsp
    suggested: (PANTHER Evolutionary analysis of coding SNPs, RRID:SCR_005145)
    SIFT is a program that predicts the functional effect of an amino acid substitution in a particular protein.
    SIFT
    suggested: (SIFT, RRID:SCR_012813)
    The rsIDs of missense SNPs extracted from NCBI dbSNP were pasted into the SIFT4G predictions tool.
    dbSNP
    suggested: (dbSNP, RRID:SCR_002338)
    Amino acid FASTA sequences of IFITM1, IFITM2, and IFITM3 proteins were copied from UniProt (https://www.uniprot.org/) [31] and inserted into the PROVEAN Protein tool with substitutions.
    https://www.uniprot.org/
    suggested: (Universal Protein Resource, RRID:SCR_002380)
    PolyPhen-2 works similarly to PROVEAN.
    PROVEAN
    suggested: (PROVEAN, RRID:SCR_002182)
    Mutation Assessor and PANTHER cSNP tools estimate the effects of the substitutions in the evolutionary base.
    Mutation Assessor
    suggested: (UMD p53 Mutation Database, RRID:SCR_006720)
    Homology modeling of wild and mutant Types of IFITM1, IFITM2, and IFITM3 proteins: Amino acid sequences (FASTA format) of wild-type protein products of IFITM1, IFITM2, and IFITM3 were obtained from UniProt [31].
    UniProt
    suggested: (UniProtKB, RRID:SCR_004426)
    I-TASSER provides the Confidence (C)-score, estimated TM-score, and estimated RMSD value for each model it creates.
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)

    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: 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.

    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.

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