Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics

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1. Version published to 10.1186/s43141-021-00152-z

   Dec 1, 2021
2. 

   ScreenIT

   Dec 3, 2020

   SciScore for 10.1101/2020.12.02.408229: (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 genome was aligned with the reference genome by NCBI Nucleotide Basic Local Alignment Search Tools (BLASTN) to identify the mutations in the Untranslated Regions (UTRs) [16].	BLASTN suggested: (BLASTN, RRID:SCR_001598)
   To assess the effect of the novel mutations, MUpro, Protein Variation Effect Analyzer (PROVEAN) and HOPE were employed [19–21].	PROVEAN suggested: (PROVEAN, RRID:SCR_002182)
   The generated structures were energetically minimized by 3D Refine and then again refined by Galaxy Refine [24, 25]. 2.4.	Galaxy suggested: (Galaxy, RRID:SCR_006281)
   1-naphthyl) ethyl] benzamide (PubChem …

   SciScore for 10.1101/2020.12.02.408229: (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 genome was aligned with the reference genome by NCBI Nucleotide Basic Local Alignment Search Tools (BLASTN) to identify the mutations in the Untranslated Regions (UTRs) [16].	BLASTN suggested: (BLASTN, RRID:SCR_001598)
   To assess the effect of the novel mutations, MUpro, Protein Variation Effect Analyzer (PROVEAN) and HOPE were employed [19–21].	PROVEAN suggested: (PROVEAN, RRID:SCR_002182)
   The generated structures were energetically minimized by 3D Refine and then again refined by Galaxy Refine [24, 25]. 2.4.	Galaxy suggested: (Galaxy, RRID:SCR_006281)
   1-naphthyl) ethyl] benzamide (PubChem CID: 24941262) is a PLPro inhibitor with a relatively low level of cytotoxicity [27].	PubChem suggested: (PubChem, RRID:SCR_004284)
   Here, we analyzed the interactions between GRL0617 and PLPro by AutoDock Vina using our previously reported methodology for exploring drug-receptor interactions [28, 29].	AutoDock suggested: (AutoDock, RRID:SCR_012746)
   , BIOVIA Discovery Studio and PyMOL Molecular Graphics System, Version 2.3.3 Schrödinger, LLC. 2.6. Analysis of ISG15-PLPro interactions: ISG15 C-terminal domain that interacts with PLPro was collected from PDB ID: 6XA9.	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: Please consider improving the rainbow (“jet”) colormap(s) used on page 21. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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 10.1101/2020.12.02.408229 on bioRxiv

   Dec 2, 2020