Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike
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SciScore for 10.1101/2020.05.05.079202: (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 curves were plotted using GraphPad Prism 8. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Structural comparisons used SHP (Stuart et al., 1979), residues forming the RBD/Fab interface were identified with PISA (Krissinel and Henrick, 2007), figures were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC). PyMOLsuggested: (PyMOL, RRID:SCR_000305)CTF-estimation with GCTF (v1.06) (Zhang, 2016) and non-template-driven particle picking was then performed within cryoSPARC v2.14.1-live followed by multiple rounds of 2D classification … SciScore for 10.1101/2020.05.05.079202: (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 curves were plotted using GraphPad Prism 8. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Structural comparisons used SHP (Stuart et al., 1979), residues forming the RBD/Fab interface were identified with PISA (Krissinel and Henrick, 2007), figures were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC). PyMOLsuggested: (PyMOL, RRID:SCR_000305)CTF-estimation with GCTF (v1.06) (Zhang, 2016) and non-template-driven particle picking was then performed within cryoSPARC v2.14.1-live followed by multiple rounds of 2D classification (Punjani et al., 2017). GCTFsuggested: (GCTF, RRID:SCR_016500)Both structures were then sharpened in cryoSPARC. cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)An initial model for the spike (structure-A) was generated using PDB ID, 6VYB (Walls et al., 2020) and rigid body fitted into the final map using COOT (Emsley and Cowtan, 2004). COOTsuggested: (Coot, RRID:SCR_014222)The model was further refined in real space with PHENIX (Liebschner et al., 2019) which resulted in a correlation coefficient of 0.84. PHENIXsuggested: (Phenix, RRID:SCR_014224)Results from OddPub: Thank you for sharing your data.
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.
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