A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2

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1. Version published to 10.1016/j.jsb.2020.107617

   Nov 1, 2020
2. 

   ScreenIT

   Jun 24, 2020

   SciScore for 10.1101/2020.06.23.164947: (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 resulting sequences were realigned with MAFFT using SARS-CoV-2 as reference.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Set-D contains human sequences of ACE2 from the 1000 human Genome project (Auton and Brooks, 2015); for this set, we used the Ensembl project (Hunt et al., 2018) and extracted the different protein haplotypes existing in the 1000 Genome Project for ACE2 using the GRCh38 human genome assembly as reference.	Ensembl suggested: (Ensembl, RRID:SCR_002344)
   Computations of the electrostatic potential surface: were performed with the Adaptive Poisson Boltzmann Solver, APBS (Baker …

   SciScore for 10.1101/2020.06.23.164947: (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 resulting sequences were realigned with MAFFT using SARS-CoV-2 as reference.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Set-D contains human sequences of ACE2 from the 1000 human Genome project (Auton and Brooks, 2015); for this set, we used the Ensembl project (Hunt et al., 2018) and extracted the different protein haplotypes existing in the 1000 Genome Project for ACE2 using the GRCh38 human genome assembly as reference.	Ensembl suggested: (Ensembl, RRID:SCR_002344)
   Computations of the electrostatic potential surface: were performed with the Adaptive Poisson Boltzmann Solver, APBS (Baker et al., 2001), in PyMol 2.0 (Schrödinger, 2015).	PyMol suggested: (PyMOL, RRID:SCR_000305)
   As computations of average H-bond graphs require the same number of amino acid residues in the graphs to be averaged, where needed we used Modeller 9.21 (Marti-Renom et al., 2000) to construct coordinates for missing amino acid residues.	Modeller suggested: (MODELLER, RRID:SCR_008395)

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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 pages 19, 20, 29 and 23. 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.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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3. 

   Version published to 10.1101/2020.06.23.164947v1 on bioRxiv

   Jun 23, 2020