Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease

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1. Version published to 10.1021/acs.jcim.1c00140

   May 3, 2021
2. 

   ScreenIT

   Jul 25, 2020

   SciScore for 10.1101/2020.07.23.218784: (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
   Histidine 64, 80, and 164 were thus named HID to indicate delta nitrogen protonation before protonation of entire protein using tleap from AmberTools 18.22 The ff14SB23 forcefield was used for proteogenic residues.	AmberTools suggested: (AmberTools, RRID:SCR_018497)
   High throughput virtual screening: Schrödinger Virtual Screening Workflow was followed using Schrödinger release 2020-1.14 ChemBridge CombiSet Library of 71,789 compounds were prepared using LigPrep with empirical pKa prediction (Epik).	LigPrep suggested: (Ligprep, RRID:SCR_016746)
   Additional analysis: For the graphical abstract, to …

   SciScore for 10.1101/2020.07.23.218784: (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
   Histidine 64, 80, and 164 were thus named HID to indicate delta nitrogen protonation before protonation of entire protein using tleap from AmberTools 18.22 The ff14SB23 forcefield was used for proteogenic residues.	AmberTools suggested: (AmberTools, RRID:SCR_018497)
   High throughput virtual screening: Schrödinger Virtual Screening Workflow was followed using Schrödinger release 2020-1.14 ChemBridge CombiSet Library of 71,789 compounds were prepared using LigPrep with empirical pKa prediction (Epik).	LigPrep suggested: (Ligprep, RRID:SCR_016746)
   Additional analysis: For the graphical abstract, to demonstrate enhanced sampling of conformational space, reweighting of the potential energy was carried out on one 200 ns simulation of the N3 bound dimer using PyReweighting toolkit.	PyReweighting suggested: None

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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 1 and 4. 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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   Read the original source
3. 

   Version published to 10.1101/2020.07.23.218784v1 on bioRxiv

   Jul 24, 2020