In silico evidence of superantigenic features in ORF8 protein from COVID-19

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   ScreenIT

   Dec 17, 2021

   SciScore for 10.1101/2021.12.14.472240: (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
   Sentences	Resources
   The signal peptide in ORF8 was predicted using SignalP 5, an algorithm software that predicts signal peptides and cleavage site [25].	SignalP suggested: (SignalP, RRID:SCR_015644)
   Basic secondary structure of ORF8 was predicted using PredictProtein, an algorithm software that predict secondary structure of proteins based on a wide array of protein features [26]	PredictProtein suggested: None
   Amino acid similarity analysis: The amino acid (aa) similarity analyses between ORF8 and TSST were performed using protein BLAST, [27] and Clustal Omega [28], with default settings.	BLAST suggested: (BLASTX, …

   SciScore for 10.1101/2021.12.14.472240: (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
   Sentences	Resources
   The signal peptide in ORF8 was predicted using SignalP 5, an algorithm software that predicts signal peptides and cleavage site [25].	SignalP suggested: (SignalP, RRID:SCR_015644)
   Basic secondary structure of ORF8 was predicted using PredictProtein, an algorithm software that predict secondary structure of proteins based on a wide array of protein features [26]	PredictProtein suggested: None
   Amino acid similarity analysis: The amino acid (aa) similarity analyses between ORF8 and TSST were performed using protein BLAST, [27] and Clustal Omega [28], with default settings.	BLAST suggested: (BLASTX, RRID:SCR_001653) Clustal Omega suggested: (Clustal Omega, RRID:SCR_001591)
   Modelling of monomeric ORF8: Model of monomeric ORF8 was developed using Galaxy TBM (33) [33], followed by energy minimization using Swiss PDB Viewer version 4.1.0 and refinement using Galaxy refine tool of Galaxy web [34].	Galaxy suggested: (Galaxy, RRID:SCR_006281)
   Ramachandran analyses were carried out using ProCheck [37].	ProCheck suggested: (PROCHECK, RRID:SCR_019043)
   Binding sites determination: Binding sites determination for Homodimer ORF8, Vβ 2.1, TRBV11-2 and monomeric ORF8 was carried using SPPIDER [38] and Meta-PPISP [39] and common binding site residues from both servers were used as binding sites residues for docking.	SPPIDER suggested: None
   The interacting amino acids residues analysis were done using PyMol version 2.4.1 [30]	PyMol suggested: (PyMOL, RRID:SCR_000305)

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   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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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.

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   Results from scite Reference Check: We found no unreliable references.

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   Version published to 10.1101/2021.12.14.472240 on bioRxiv

   Dec 14, 2021