D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1

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1. Version published to 10.1016/j.csbj.2022.01.017

   Jan 1, 2022
2. 

   ScreenIT

   Mar 28, 2021

   SciScore for 10.1101/2021.03.26.437194: (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
   2.1 Bioinformatic Methods: A total of26,656 sequences of ORF3a protein deposited in NCBI database as on Nov 17, 2020 were considered for the bioinformatics analysis.	NCBI suggested: (NCBI, RRID:SCR_006472)
   These structures were aligned using the BLAST algorithm on the NCBI website.	BLAST suggested: (BLASTX, RRID:SCR_001653)
   PROVEAN score of each mutation was determined using PROVEAN web server [24].	PROVEAN suggested: (PROVEAN, RRID:SCR_002182)
   2.3 Molecular dynamics simulation: We performed classical Molecular Dynamics (MD) simulation in AMBER20[28]using AMBER ff14sb force field[29].	AMBER suggested…

   SciScore for 10.1101/2021.03.26.437194: (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
   2.1 Bioinformatic Methods: A total of26,656 sequences of ORF3a protein deposited in NCBI database as on Nov 17, 2020 were considered for the bioinformatics analysis.	NCBI suggested: (NCBI, RRID:SCR_006472)
   These structures were aligned using the BLAST algorithm on the NCBI website.	BLAST suggested: (BLASTX, RRID:SCR_001653)
   PROVEAN score of each mutation was determined using PROVEAN web server [24].	PROVEAN suggested: (PROVEAN, RRID:SCR_002182)
   2.3 Molecular dynamics simulation: We performed classical Molecular Dynamics (MD) simulation in AMBER20[28]using AMBER ff14sb force field[29].	AMBER suggested: (AMBER, RRID:SCR_016151)
   The model was then evaluated using the SAVES v5.0 server, where Ramachandran plot and ERRAT analyses were performed[38,39].	SAVES suggested: (SAVES, RRID:SCR_018219)

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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.
   • 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.

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3. 

   Version published to 10.1101/2021.03.26.437194 on bioRxiv

   Mar 26, 2021