Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots
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SciScore for 10.1101/2021.04.13.439743: (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 These structures included the SARS-CoV-2 S-RBD complexes with class I B38 antibody (Figure 1A), class II P2B-2F6 antibody (Figure 1B), and class III EY6A and S304 antibodies (Figure 1C). S304suggested: (Abcam Cat# ab63554, RRID:AB_1141794)Software and Algorithms Sentences Resources MD Simulations of the SARS-CoV-2 S-RBD Complexes with Antibodies: All-atom MD simulations were performed for an N, P, T ensemble in explicit solvent using NAMD 2.13 package77 with CHARMM36 force field. NAMDsuggested: (NAMD, RRID:SCR_014894)Principal component analysis (PCA) of MD trajectories using the CARMA package. CARMAsuggeste…SciScore for 10.1101/2021.04.13.439743: (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 These structures included the SARS-CoV-2 S-RBD complexes with class I B38 antibody (Figure 1A), class II P2B-2F6 antibody (Figure 1B), and class III EY6A and S304 antibodies (Figure 1C). S304suggested: (Abcam Cat# ab63554, RRID:AB_1141794)Software and Algorithms Sentences Resources MD Simulations of the SARS-CoV-2 S-RBD Complexes with Antibodies: All-atom MD simulations were performed for an N, P, T ensemble in explicit solvent using NAMD 2.13 package77 with CHARMM36 force field. NAMDsuggested: (NAMD, RRID:SCR_014894)Principal component analysis (PCA) of MD trajectories using the CARMA package. CARMAsuggested: (CARMA, RRID:SCR_004999)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 pages 64 and 12. 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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