Discovery of COVID-19 Inhibitors Targeting the SARS-CoV-2 Nsp13 Helicase
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SciScore for 10.1101/2020.08.09.243246: (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 resulting SARS-CoV2 models were then energy minimized by maintaining the crystallographic orientation for common atoms using Phenix, while stereochemical issues caused by mutation were corrected using COOT. Phenixsuggested: (Phenix, RRID:SCR_014224)COOTsuggested: (Coot, RRID:SCR_014222)Results from OddPub: We did not detect open data. We also did …
SciScore for 10.1101/2020.08.09.243246: (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 resulting SARS-CoV2 models were then energy minimized by maintaining the crystallographic orientation for common atoms using Phenix, while stereochemical issues caused by mutation were corrected using COOT. Phenixsuggested: (Phenix, RRID:SCR_014224)COOTsuggested: (Coot, RRID:SCR_014222)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 Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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SciScore for 10.1101/2020.08.09.243246: (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 Mutation of the MERS (5WWP) crystal structure to the SARS-CoV2 sequence was performed in COOT. COOTsuggested: (Coot, RRID:SCR_014222)Energy minimization was performed in Phenix, followed by optimization of stereochemistry in COOT for several rounds. Phenixsuggested: (Phenix, RRID:SCR_014224)We screened the identified substrate binding sites in each Nsp13 model using an implementation of AutoDock Vina45 on the Drug Discovery Portal at TACC.46 The ZINC47,48 drugs in Trials (9,270 compounds) Library, the Enamine-PC (84,359 compounds), and Enamine-AC (876,985 compounds) were used in … SciScore for 10.1101/2020.08.09.243246: (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 Mutation of the MERS (5WWP) crystal structure to the SARS-CoV2 sequence was performed in COOT. COOTsuggested: (Coot, RRID:SCR_014222)Energy minimization was performed in Phenix, followed by optimization of stereochemistry in COOT for several rounds. Phenixsuggested: (Phenix, RRID:SCR_014224)We screened the identified substrate binding sites in each Nsp13 model using an implementation of AutoDock Vina45 on the Drug Discovery Portal at TACC.46 The ZINC47,48 drugs in Trials (9,270 compounds) Library, the Enamine-PC (84,359 compounds), and Enamine-AC (876,985 compounds) were used in high-throughput virtual screening of the five targets. AutoDocksuggested: (AutoDock, RRID:SCR_012746)Only the ZINC library “in-Trials” subset contains drugs currently approved for human use. ZINCsuggested: (Zinc, RRID:SCR_008596)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: We did not find any issues relating to colormaps.
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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