Structural characterization of nonstructural protein 1 from SARS-CoV-2
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Article activity feed
-
-
SciScore for 10.1101/2020.09.08.288191: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Final model was produced by the cycle of manual model building and refinement using Phenix.refine and Coot [30, 31]. Cootsuggested: (Coot, RRID:SCR_014222)Structure analysis and homology-modeling: Electrostatic potential surfaces were calculated using Pymol using APBS[21]. Pymolsuggested: (PyMOL, RRID:SCR_000305)· Structure similarity searches of the Protein Data Bank were performed using the Dali server [22]. Dalisuggested: (Dali Server, RRID:SCR_013433)Secondary structure … SciScore for 10.1101/2020.09.08.288191: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Final model was produced by the cycle of manual model building and refinement using Phenix.refine and Coot [30, 31]. Cootsuggested: (Coot, RRID:SCR_014222)Structure analysis and homology-modeling: Electrostatic potential surfaces were calculated using Pymol using APBS[21]. Pymolsuggested: (PyMOL, RRID:SCR_000305)· Structure similarity searches of the Protein Data Bank were performed using the Dali server [22]. Dalisuggested: (Dali Server, RRID:SCR_013433)Secondary structure prediction of Nsp1 homologues was done using PSIPRED [26] PSIPREDsuggested: (PSIPRED, RRID:SCR_010246)Homology modeling of MERS-CoV was performed by I-TASSER using the crystal structure of SARS-CoV-2 Nsp113-127 as the threading template [32, 33]. I-TASSERsuggested: (I-TASSER, RRID:SCR_014627)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).
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: Please consider improving the rainbow (“jet”) colormap(s) used on page 18. 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.
-
