Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7
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Abstract
Using force-field and DFT based computational approaches, we investigate the reason behind the increased virulence of alpha variant of SARS-CoV-2. The binding free energies for spike proteins of wild and alpha variants with hACE-2 receptor were estimated in this study.
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SciScore for 10.1101/2021.01.25.428190: (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 A similar protocol has been followed for mt-spike:ACE-2 complex except that before processing the PDB structure for the MD input file preparation, the two aforementioned mutations were introduced in the spike protein using Mutagenesis module of PyMOL software. PyMOLsuggested: (PyMOL, RRID:SCR_000305)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. …SciScore for 10.1101/2021.01.25.428190: (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 A similar protocol has been followed for mt-spike:ACE-2 complex except that before processing the PDB structure for the MD input file preparation, the two aforementioned mutations were introduced in the spike protein using Mutagenesis module of PyMOL software. PyMOLsuggested: (PyMOL, RRID:SCR_000305)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: 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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