Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M pro
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Article activity feed
-
-
SciScore for 10.1101/2020.05.29.123190: (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 PyMOL (version 2.4) [64] was used to remove any non-protein molecule and to reconstitute the biological unit as chains A and B. PyMOLsuggested: (PyMOL, RRID:SCR_000305)A local BLAST database was then set up for these sequences using the makeblastdb command available from the BLAST+ application (version 2.8.1) [65]. BLASTsuggested: (BLASTX, RRID:SCR_001653)BLAST+suggested: (Japan Bioinformatics, RRID:SCR_012250)Homology modelling, pH adjustment and analysis of residue interactions: PIR-formatted target-template sequence alignment files were generated for each mutant using the BioPython … SciScore for 10.1101/2020.05.29.123190: (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 PyMOL (version 2.4) [64] was used to remove any non-protein molecule and to reconstitute the biological unit as chains A and B. PyMOLsuggested: (PyMOL, RRID:SCR_000305)A local BLAST database was then set up for these sequences using the makeblastdb command available from the BLAST+ application (version 2.8.1) [65]. BLASTsuggested: (BLASTX, RRID:SCR_001653)BLAST+suggested: (Japan Bioinformatics, RRID:SCR_012250)Homology modelling, pH adjustment and analysis of residue interactions: PIR-formatted target-template sequence alignment files were generated for each mutant using the BioPython library (Version 1.76) [66] within ad hoc Python scripts for use in MODELLER (version 9.22) [67]. BioPythonsuggested: (Biopython, RRID:SCR_007173)Pythonsuggested: (IPython, RRID:SCR_001658)MODELLERsuggested: (MODELLER, RRID:SCR_008395)For visualising the overall interactions at given residue positions, the Arpeggio tool [69] was used to programmatically generate the inter-residue interactions, before computing their sums using an in-house Python script. Arpeggiosuggested: (Arpeggio, RRID:SCR_010876)Molecular dynamics simulations: All-atom protein MD simulations were run for the protonated dimers using GROMACS (version 2016.1) [71] at the Center for High Performance Computing (CHPC). GROMACSsuggested: (GROMACS, RRID:SCR_014565)The generated data was then visualised and analysed using various open source Python libraries, such as matplotlib [72], Seaborn, Pandas [73], NumPy [74], SciPy [75], MDTraj [76] and NGLview [77]. matplotlibsuggested: (MatPlotLib, RRID:SCR_008624)NumPysuggested: (NumPy, RRID:SCR_008633)SciPysuggested: (SciPy, RRID:SCR_008058)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 17 and 15. 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.
- No funding statement was detected.
- No protocol registration statement was detected.
-
