Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion
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SciScore for 10.1101/2021.12.12.472313: (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 not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Several limitations and caveats apply to our computed structural models and analyses. First, post-translational modifications such as glycosylation, which may often be a key element of Spike structure, are not considered in our protein-only models. Many experimental structure determinations also exclude these glycans, and multiple X-ray structures show that …
SciScore for 10.1101/2021.12.12.472313: (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 not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Several limitations and caveats apply to our computed structural models and analyses. First, post-translational modifications such as glycosylation, which may often be a key element of Spike structure, are not considered in our protein-only models. Many experimental structure determinations also exclude these glycans, and multiple X-ray structures show that the ACE2-binding interface does not explicitly involve glycans. However, some glycosylation patterns do affect binding of certain antibodies. Second, we do not include explicit interfacial water molecules in our modeling procedures. There were no major water-mediated interactions observed experimentally in the complexes we analyzed in detail. However, it is conceivable that new water-mediated interactions have been missed. Both limitations can be addressed by using the models reported here as starting points for more computationally-expensive modeling approaches (such as molecular dynamics simulations) with appropriately glycosylated amino acid sidechains.50 In addition to these limitations inherent to modeling procedures, there are well-known limitations of the energy functions used for scoring and energy evaluations plus the limited conformational sampling that is performed in the interest of computational efficiency. Because the overall structure of omRBD is likely to be highly similar to the Wuhan-Hu-1 RBD, limited sampling around the conformations observed in experimentally-derived structures represents a reasonable t...
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.
Results from scite Reference Check: We found no unreliable references.
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