Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

Article activity feed

1. Version published to 10.1038/s41467-020-18709-w

   Oct 7, 2020
2. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.27.118117: (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
   2020); heterocyclic electrophiles (Keeley et al., 2019); and the SpotFinder library (Bajusz and Keserü).	SpotFinder suggested: (Spotfinder, RRID:SCR_000085)
   Further analysis was performed with XChemExplorer (Krojer et al., 2017): electron density maps were generated with Dimple (Keegan et al., 2015); ligand-binding events were identified using PanDDA (Pearce et al., 2017) (both the released version 0.2 and the pre-release development version (https://github.com/ConorFWild/pandda)); …

   SciScore for 10.1101/2020.05.27.118117: (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
   2020); heterocyclic electrophiles (Keeley et al., 2019); and the SpotFinder library (Bajusz and Keserü).	SpotFinder suggested: (Spotfinder, RRID:SCR_000085)
   Further analysis was performed with XChemExplorer (Krojer et al., 2017): electron density maps were generated with Dimple (Keegan et al., 2015); ligand-binding events were identified using PanDDA (Pearce et al., 2017) (both the released version 0.2 and the pre-release development version (https://github.com/ConorFWild/pandda)); ligands were modelled into PanDDA-calculated event maps using Coot (Emsley et al., 2010); restraints were calculated with ACEDRG or GRADE (Long et al., 2017, Smart et al., 2010); and structures were refined with Refmac (Murshudov et al., 2011) and Buster (Bricogne et al., 2017).	Coot suggested: (Coot, RRID:SCR_014222) Refmac suggested: (Refmac, RRID:SCR_014225)

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   Results from OddPub: Thank you for sharing your code and 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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04353128	Recruiting	Efficacy of Melatonin in the Prophylaxis of Coronavirus Dise…

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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: We did not find any issues relating to colormaps.

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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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3. 

   Version published to 10.1101/2020.05.27.118117v1 on bioRxiv

   May 27, 2020