Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling

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1. Version published to 10.1021/acs.jcim.1c00766

   Sep 22, 2021
2. 

   ScreenIT

   Jun 18, 2021

   SciScore for 10.1101/2021.06.15.448568: (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
   All-atom MD simulations were performed for an N, P, T ensemble in explicit solvent using NAMD 2.13 package55 with CHARMM36 force field.	NAMD suggested: (NAMD, RRID:SCR_014894)
   Functional Dynamics and Collective Motions: We performed principal component analysis (PCA) of reconstructed trajectories derived from CABS-CG simulations using the CARMA package60 and also determined the essential slow mode profiles using elastic network models (ENM) analysis.61-63 Two elastic network models: Gaussian network model (GNM) and Anisotropic network model (ANM) approaches were used to compute the …

   SciScore for 10.1101/2021.06.15.448568: (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
   All-atom MD simulations were performed for an N, P, T ensemble in explicit solvent using NAMD 2.13 package55 with CHARMM36 force field.	NAMD suggested: (NAMD, RRID:SCR_014894)
   Functional Dynamics and Collective Motions: We performed principal component analysis (PCA) of reconstructed trajectories derived from CABS-CG simulations using the CARMA package60 and also determined the essential slow mode profiles using elastic network models (ENM) analysis.61-63 Two elastic network models: Gaussian network model (GNM) and Anisotropic network model (ANM) approaches were used to compute the amplitudes of isotropic thermal motions and directionality of anisotropic motions.	CARMA suggested: (CARMA, RRID:SCR_004999)
   78 The g_correlation tool in the Gromacs 3.3 package was used that allows computation of both linear or non-linear generalized correlation coefficients.	Gromacs suggested: (GROMACS, RRID:SCR_014565)
   86 Network graph calculations were performed using the python package NetworkX.87 The Girvan-Newman algorithm88,89 is used to identify local communities.	python suggested: (IPython, RRID:SCR_001658)

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   Results from OddPub: Thank you for sharing your data.

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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 49, 47, 13 and 7. 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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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
3. 

   Version published to 10.1101/2021.06.15.448568v1 on bioRxiv

   Jun 15, 2021