Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide
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SciScore for 10.1101/2020.12.03.410472: (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 system was equilibrated with NAMD version 2.12 37 following a multi-step protocol during which the backbone atoms of the SARS-CoV-2-FP as well as Ca2+ ions in the solution were first harmonically constrained and subsequently gradually released in four steps (totaling ~3ns), changing the restrain force constants kF from 1, to 0.5, to 0.1 kcal/ (mol Å2), and 0 kcal/ (mol Å2). NAMDsuggested: (NAMD, RRID:SCR_014894)After this phase, the velocities of all atoms of the system were reset, and ensemble MD runs were initiated with OpenMM version 7.4. OpenMMsuggested: (OpenMM, RRID:SCR_000436)Resu…
SciScore for 10.1101/2020.12.03.410472: (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 system was equilibrated with NAMD version 2.12 37 following a multi-step protocol during which the backbone atoms of the SARS-CoV-2-FP as well as Ca2+ ions in the solution were first harmonically constrained and subsequently gradually released in four steps (totaling ~3ns), changing the restrain force constants kF from 1, to 0.5, to 0.1 kcal/ (mol Å2), and 0 kcal/ (mol Å2). NAMDsuggested: (NAMD, RRID:SCR_014894)After this phase, the velocities of all atoms of the system were reset, and ensemble MD runs were initiated with OpenMM version 7.4. OpenMMsuggested: (OpenMM, RRID:SCR_000436)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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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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