Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease

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1. Version published to 10.1021/acs.biochem.0c00462

   Sep 15, 2020
2. 

   ScreenIT

   Jun 8, 2020

   SciScore for 10.1101/2020.05.15.097493: (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
   Open reading frames in these high-quality full genomes were compared with a reference Mpro nucleotide sequence (WT, RefSeq: NC 045512.2, loc: 10,055–10,972), to extract Mpro sequences of at least 80% similarity using a script written in Python v3.7.0 (35).	Python suggested: (IPython, RRID:SCR_001658)
   Full genome alignments were performed using MUSCLE (14) on the complete set of non-synonymous Mpro mutants as well as reference WT, bat, and pangolin sequences.	MUSCLE suggested: (MUSCLE, RRID:SCR_011812)
   Trees were generated in MEGA X (15), using the Neighbor-Joining method (37); a bootstrap test …

   SciScore for 10.1101/2020.05.15.097493: (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
   Open reading frames in these high-quality full genomes were compared with a reference Mpro nucleotide sequence (WT, RefSeq: NC 045512.2, loc: 10,055–10,972), to extract Mpro sequences of at least 80% similarity using a script written in Python v3.7.0 (35).	Python suggested: (IPython, RRID:SCR_001658)
   Full genome alignments were performed using MUSCLE (14) on the complete set of non-synonymous Mpro mutants as well as reference WT, bat, and pangolin sequences.	MUSCLE suggested: (MUSCLE, RRID:SCR_011812)
   Trees were generated in MEGA X (15), using the Neighbor-Joining method (37); a bootstrap test (38) of 1000 replicates was performed, and distances were calculated using the Maximum Composite Likelihood model (38).	MEGA suggested: (Mega BLAST, RRID:SCR_011920)
   Initial variant protein structures were predicted using MODELLER 9.23 (30), using the 6Y2E structure as a template; three rounds of annealing and MD refinement were performed using the “slow” optimization level for each.	MODELLER suggested: (MODELLER, RRID:SCR_008395)
   Table of Contents:	Contents suggested: None

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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 10.1101/2020.05.15.097493 on bioRxiv

   May 15, 2020