SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential
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SciScore for 10.1101/2020.12.10.420109: (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 Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)This analysis was performed using the cluster centers and the equilibrium probabilities derived from the MSMs built on the residue level SASA described above. MSMssuggested: (MSMS, RRID:SCR_003532)Sequences alignment was performed on Clustal Omega server (56). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Sequence alignment was visualized, and the sequence conservation score was generated using Jalview 2 software (57). Jalviewsuggested: …SciScore for 10.1101/2020.12.10.420109: (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 Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)This analysis was performed using the cluster centers and the equilibrium probabilities derived from the MSMs built on the residue level SASA described above. MSMssuggested: (MSMS, RRID:SCR_003532)Sequences alignment was performed on Clustal Omega server (56). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Sequence alignment was visualized, and the sequence conservation score was generated using Jalview 2 software (57). Jalviewsuggested: (Jalview, RRID:SCR_006459)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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SciScore for 10.1101/2020.12.10.420109: (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 Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)Markov State Models A Markov State Model (MSM) is a statistical framework for analyzing molecular dynamics simulations that provides a network representation of a free energy landscape. ( 37, 48, 49) To quantify cryptic pocket opening across the homologs and changes between monomeric Nsp16 and the Nsp10/Nsp16 complex, we performed … SciScore for 10.1101/2020.12.10.420109: (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 Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)Markov State Models A Markov State Model (MSM) is a statistical framework for analyzing molecular dynamics simulations that provides a network representation of a free energy landscape. ( 37, 48, 49) To quantify cryptic pocket opening across the homologs and changes between monomeric Nsp16 and the Nsp10/Nsp16 complex, we performed several measurements that rely on MSMs built based on the simulation data. MSMssuggested: (MSMS, RRID:SCR_003532)Sequences alignment was performed on Clustal Omega server (56). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Sequence alignment was visualized, and the sequence conservation score was generated using Jalview 2 software (57). Jalviewsuggested: (Jalview, RRID:SCR_006459)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.
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