E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody
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SciScore for 10.1101/2021.06.23.449627: (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 Preparation of spike mutants, spike-ACE2, and spike-antibody complexes: Recently, I refined the crystal structure of the SARS-CoV2 RBD-ACE2 complex (PDB ID: 6M0J19) using extensive molecular dynamics simulation, which was used as a starting structure for the present study. spike-ACE2suggested: NoneThe recently resolved crystal structure of the SARS-CoV2 spike RBD complexed with a neutralizing antibody (B38) was considered for the study (PDB ID:7BZ5). B38suggested: NoneCalculation of the potential of mean force (PMF) for wild-type and mutant spike RBD to ACE2 and B38 antibody: The optimized wild-type and … SciScore for 10.1101/2021.06.23.449627: (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 Preparation of spike mutants, spike-ACE2, and spike-antibody complexes: Recently, I refined the crystal structure of the SARS-CoV2 RBD-ACE2 complex (PDB ID: 6M0J19) using extensive molecular dynamics simulation, which was used as a starting structure for the present study. spike-ACE2suggested: NoneThe recently resolved crystal structure of the SARS-CoV2 spike RBD complexed with a neutralizing antibody (B38) was considered for the study (PDB ID:7BZ5). B38suggested: NoneCalculation of the potential of mean force (PMF) for wild-type and mutant spike RBD to ACE2 and B38 antibody: The optimized wild-type and mutant (E484K and N501Y) SARS-CoV2 RBD complexed with ACE2 and B38 were immersed in a triclinic box filled with TIP3P water such that the minimum distance between any protein atom and box edges was > 10 ◻. ACE2suggested: NoneSoftware and Algorithms Sentences Resources Equilibrium simulations of wild-type and mutant SARS-CoV2 spike RBD-ACE2 and RBD-antibody complexes: All the simulations were performed using GROMACS 2018.122,23 packages using the AMBER99SB-ILDN force field. 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 22. 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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