Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes

Article activity feed

1. Version published to 10.1021/acs.jcim.1c01240

   Dec 16, 2021
2. 

   ScreenIT

   Sep 23, 2021

   SciScore for 10.1101/2021.09.16.460716: (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 adjusted conformation is consistent with the newly released conformation on the I-TASSER website.	I-TASSER suggested: (I-TASSER, RRID:SCR_014627)
   Molecular Dynamics Simulations: All CG MD simulations were performed using GROMACS version 2019.2 (61) and with Martini 2.2 force field parameters (62, 63) and the ELNEDYN elastic network model on monomers, using a force constant of 500 kJ/(mol•nm2) and a distance cutoff of 0.9 nm.	GROMACS suggested: (GROMACS, RRID:SCR_014565)

   ---

   Results from OddPub: Thank you for sharing your code.

   ---

   Results from LimitationRecognizer: We detected the following …

   SciScore for 10.1101/2021.09.16.460716: (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 adjusted conformation is consistent with the newly released conformation on the I-TASSER website.	I-TASSER suggested: (I-TASSER, RRID:SCR_014627)
   Molecular Dynamics Simulations: All CG MD simulations were performed using GROMACS version 2019.2 (61) and with Martini 2.2 force field parameters (62, 63) and the ELNEDYN elastic network model on monomers, using a force constant of 500 kJ/(mol•nm2) and a distance cutoff of 0.9 nm.	GROMACS suggested: (GROMACS, RRID:SCR_014565)

   ---

   Results from OddPub: Thank you for sharing your code.

   ---

   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Another possible limitation of our simulations is the use of Martini CG force field 2.2, which may limit the protein conformational changes due to the elastic network (53), such as the RBD opening in our simulations, and may tend to excessive protein aggregation because of excessive inter-protein interactions. Future simulations will try the latest Martini force fields 3.0 (54).

   ---

   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: 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.

   ---

   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.

   ---

   Results from scite Reference Check: We found no unreliable references.

   ---

   Read the original source
3. 

   Version published to 10.1101/2021.09.16.460716v1 on bioRxiv

   Sep 20, 2021