SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction
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SciScore for 10.1101/2021.07.15.452507: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization The starting configuration was the same for each independent run, but the random seed for the velocities in each run was randomly assigned, resulting in independent behaviors. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Because the system changed, the force field files had to be regenerated using AmberTools (44) as described previously (2). AmberToolssuggested: (AmberTools, RRID:SCR_018497)A total of 18 pulling simulations were performed at three different pulling rates (1 nm/ns, 5 nm/ns and 10 nm/ns) on the four truncated structures using Gromacs 2019.1 (51). GromacsSciScore for 10.1101/2021.07.15.452507: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization The starting configuration was the same for each independent run, but the random seed for the velocities in each run was randomly assigned, resulting in independent behaviors. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Because the system changed, the force field files had to be regenerated using AmberTools (44) as described previously (2). AmberToolssuggested: (AmberTools, RRID:SCR_018497)A total of 18 pulling simulations were performed at three different pulling rates (1 nm/ns, 5 nm/ns and 10 nm/ns) on the four truncated structures using Gromacs 2019.1 (51). Gromacssuggested: (GROMACS, RRID:SCR_014565)The hydrogen bonding interaction bitmap was recreated in python using matplotlib (53) in order to add labels for donor acceptor pairs and calculate the percent occupancy of hydrogen bonds across the simulation (script available in SI). matplotlibsuggested: (MatPlotLib, RRID:SCR_008624)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.
Results from scite Reference Check: We found no unreliable references.
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