SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern
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SciScore for 10.1101/2021.07.12.452002: (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 All mutations, including the “reference” D614G, are introduced using the “mutations wizard” in the PyMOL molecular modeling package (Schrodinger LLC): rotamers of non-glycine side chains are chosen from the first suggested option for S protomer A, and then, where possible, we have sought to adopt the same rotamers for protomers B and C. PyMOLsuggested: (PyMOL, RRID:SCR_000305)On each glycosylated S protein variant, we conduct 4 independently replicated atomistic molecular dynamics simulations (MD), using the AMBER package (version 18): each replica consists of two 300-step rounds of … SciScore for 10.1101/2021.07.12.452002: (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 All mutations, including the “reference” D614G, are introduced using the “mutations wizard” in the PyMOL molecular modeling package (Schrodinger LLC): rotamers of non-glycine side chains are chosen from the first suggested option for S protomer A, and then, where possible, we have sought to adopt the same rotamers for protomers B and C. PyMOLsuggested: (PyMOL, RRID:SCR_000305)On each glycosylated S protein variant, we conduct 4 independently replicated atomistic molecular dynamics simulations (MD), using the AMBER package (version 18): each replica consists of two 300-step rounds of minimization, 2.069 ns preproduction, and 1 µs production. AMBERsuggested: (AMBER, RRID:SCR_016151)Constant pressure is enforced via Berendsen’s barostat [30] with a 1 ps relaxation time, whereas temperature is stabilized by Langevin’s thermostat[31] with a 5 ps−1 collision frequency. Langevin’ssuggested: NoneResults 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: 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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