Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design
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Abstract
The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19.
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SciScore for 10.1101/2020.11.03.366609: (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 Homologous Sequence Analysis: Sequence alignments were done using BLAST with default settings and BLOSUM62 distance matrix, requesting the most similar 1000 hits from UniProtKB. BLASTsuggested: (BLASTX, RRID:SCR_001653)UniProtKBsuggested: (UniProtKB, RRID:SCR_004426)9 Missing residues and the I570V mutagenesis were constructed in pymol. pymolsuggested: (PyMOL, RRID:SCR_000305)These constraints were subsequently progressively reduced and removed during the next 20 ns, using the colvar function implemented in NAMD. NAMDsuggested: (NAMD, RRID:SCR_014894)To compare simulation results obtained … SciScore for 10.1101/2020.11.03.366609: (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 Homologous Sequence Analysis: Sequence alignments were done using BLAST with default settings and BLOSUM62 distance matrix, requesting the most similar 1000 hits from UniProtKB. BLASTsuggested: (BLASTX, RRID:SCR_001653)UniProtKBsuggested: (UniProtKB, RRID:SCR_004426)9 Missing residues and the I570V mutagenesis were constructed in pymol. pymolsuggested: (PyMOL, RRID:SCR_000305)These constraints were subsequently progressively reduced and removed during the next 20 ns, using the colvar function implemented in NAMD. NAMDsuggested: (NAMD, RRID:SCR_014894)To compare simulation results obtained with MD, we also carried out MD simulations using GROMACS 201818–21 with the Amber ff99+ parmbsc0+chioL3 force field22,23 for ssRNA and Amber14SB24 for the helicase. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Ambersuggested: (AMBER, RRID:SCR_016151)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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