Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein
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SciScore for 10.1101/2020.06.11.146522: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
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 …
SciScore for 10.1101/2020.06.11.146522: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 24 and 3. 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.
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SciScore for 10.1101/2020.06.11.146522: (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
Antibodies Sentences Resources This is in agreement with structural data reporting the “up” conformation as a requirement for C-terminal domain-1 (CTD1) neutralization by host antibodies. domain-1 (CTD1suggested: None60–62 In addition, 4A8 and 1A9 have been found to engage with the NTD and CD, respectively.51,57 To quantify the effects of glycan shielding on these epitopes, we calculated each epitope’s ASA at two probe radii, 7.2 and 18.6 Å, which approximate the size of antibody hypervariable loop and variable fragments domains, respectively (Figures 4A and 4B, … SciScore for 10.1101/2020.06.11.146522: (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
Antibodies Sentences Resources This is in agreement with structural data reporting the “up” conformation as a requirement for C-terminal domain-1 (CTD1) neutralization by host antibodies. domain-1 (CTD1suggested: None60–62 In addition, 4A8 and 1A9 have been found to engage with the NTD and CD, respectively.51,57 To quantify the effects of glycan shielding on these epitopes, we calculated each epitope’s ASA at two probe radii, 7.2 and 18.6 Å, which approximate the size of antibody hypervariable loop and variable fragments domains, respectively (Figures 4A and 4B, full data provided in Table S8). 1A9suggested: NoneConsidering the bottom part of the RBD , the epitope recognized by the CR3022 antibody is found to be almost completely shielded in Open ( 69 % /94 % ) and not accessible at all in Closed. CR3022suggested: NoneSoftware and Algorithms Sentences Resources These models were built in three steps based on three main topological domains, as described in the Materials and Methods: the “head,” comprising S1/S2 subunits until residue 1140; the “stalk,” comprising HR2 and TM domains (residues 1141–1234); and the CT (residues 1235–1273) (Figure 1A). Methodssuggested: NoneWe make available through the NSF MolSSI and BioExcel COVID-19 Molecular Structure and Therapeutics site ( https://covid.molssi.org/ ) our structures , models , input files , and trajectories to enable other groups to use and explore this dynamic system in atomic detail. BioExcelsuggested: NoneThe alignment between the cryo-EM structure and the FASTA sequence of SARS-CoV-2 spike ( QHD43416.1)70 used by Modeller was generated using Clustal Omega.71 The top models were further visually inspected to discard those in which loops were entangled in a knot or clashed with the rest of the structure. Modellersuggested: (MODELLER, SCR_008395)The CT of the S protein ( residues 1235–1273 ) was modeled using the i-TASSER software. i-TASSERsuggested: (I-TASSER, SCR_014627)All-atom MD simulations were conducted on the Frontera computing system at the Texas Advanced Computing Center ( TACC ) using NAMD 2.14.35 The systems were initially relaxed through a series of minimization , melting ( for the membrane) , and equilibration cycles . NAMDsuggested: (NAMD, SCR_014894)PCA was performed using the sklearn.decomposition.PCA function in the Scikit-learn library using python3.6.9.97 First , all simulations were aligned with mdtraj98 onto the same initial coordinates using Cα atoms of chain-A central scaffold ( residues 747–783 and 920–1032) . Scikit-learnsuggested: (scikit-learn, SCR_002577)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 OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog).
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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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