Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies
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SciScore for 10.1101/2021.05.10.443519: (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 Modeling of fully glycosylated SARS-CoV-2 S protein–antibody complex structures: As reported in our previous work16-17, we have modeled a fully glycosylated full-length SARS-CoV-2 S protein structure by using a combination of computational modeling tools including GALAXY protein modeling suite18-20 for building missing residues and domains, ISOLDE21 for model refinement against experimental density maps, and CHARMM-GUI Glycan Reader & Modeler22-24 and Membrane Builder25-28 for building glycans and a viral membrane. GALAXYsuggested: (Galaxy, RRID:SCR_006281)All simulations were performed … SciScore for 10.1101/2021.05.10.443519: (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 Modeling of fully glycosylated SARS-CoV-2 S protein–antibody complex structures: As reported in our previous work16-17, we have modeled a fully glycosylated full-length SARS-CoV-2 S protein structure by using a combination of computational modeling tools including GALAXY protein modeling suite18-20 for building missing residues and domains, ISOLDE21 for model refinement against experimental density maps, and CHARMM-GUI Glycan Reader & Modeler22-24 and Membrane Builder25-28 for building glycans and a viral membrane. GALAXYsuggested: (Galaxy, RRID:SCR_006281)All simulations were performed using the input files generated by CHARMM-GUI38-40, and we used GROMACS 2018.641 for both equilibration and production with the LINCS algorithm42. GROMACSsuggested: (GROMACS, RRID:SCR_014565)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: Please consider improving the rainbow (“jet”) colormap(s) used on page 6. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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