Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism

Article activity feed

1. 

   ScreenIT

   Jun 4, 2020

   SciScore for 10.1101/2020.03.04.976027: (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
   2.2 Sequence analysis and phylogenetic tree calculation: MAFFT 7.450 was used to align the whole genome sequences and the protein sequences of viral RBDs [5] (Supplementary Materials 1).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Prediction of the N-Glycosylation sites was made for all studied ACE2 sequences using NetNGlyc server (https://www.cbs.dtu.dk/services/NetNGlyc/).	NetNGlyc suggested: (NetNGlyc, RRID:SCR_001570)
   For the RBD sequences, the best substitution model for maximum likelihood (ML) calculation was selected using a model selection tool implemented on MEGA 6 software based on the …

   SciScore for 10.1101/2020.03.04.976027: (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
   2.2 Sequence analysis and phylogenetic tree calculation: MAFFT 7.450 was used to align the whole genome sequences and the protein sequences of viral RBDs [5] (Supplementary Materials 1).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Prediction of the N-Glycosylation sites was made for all studied ACE2 sequences using NetNGlyc server (https://www.cbs.dtu.dk/services/NetNGlyc/).	NetNGlyc suggested: (NetNGlyc, RRID:SCR_001570)
   For the RBD sequences, the best substitution model for maximum likelihood (ML) calculation was selected using a model selection tool implemented on MEGA 6 software based on the lowest BIC score.	MEGA suggested: (Mega BLAST, RRID:SCR_011920)
   The template sequences of the ligand (spike protein) and the receptor (ACE2) were aligned locally with the target sequences using the program Water from the EMBOSS package [12]	EMBOSS suggested: (EMBOSS, RRID:SCR_008493)
   Modeller version 9.22 [14] was then used to predict the complex model of each spike protein with the ACE2 using a slow refining protocol.	Modeller suggested: (MODELLER, RRID:SCR_008395)

   ---

   Results from OddPub: Thank you for sharing your data.

   ---

   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.

   ---

   Results from TrialIdentifier: No clinical trial numbers were referenced.

   ---

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

   ---

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

   ---

   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.

   ---

   Read the original source
2. Version published to 10.1016/j.bbrc.2020.05.028

   Jun 1, 2020
3. 

   Version published to 10.1101/2020.03.04.976027 on bioRxiv

   Mar 7, 2020