Modeling SARS-CoV-2 spike/ACE2 protein–protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context
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SciScore for 10.1101/2021.05.26.445422: (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
Recombinant DNA Sentences Resources Furthermore, the FoldX AnalyseComplex assay was used for determining the binding affinity between SARS-CoV-2 spike RBD and the ACE2 structurally related receptors ACE, THOP1, and NLN, identified through pGenTHREADER and/or ITASSER analyses. pGenTHREADERsuggested: NoneSoftware and Algorithms Sentences Resources With this aim, the amino acid sequence of ACE2 (NP_001358344.1) was used as query sequence for running pGenThreader (http://bioinf.cs.ucl.ac.uk/psipred/) and I-Tasser (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) to screen the Protein Data Bank (PDB), searching for ACE2 structurally related … SciScore for 10.1101/2021.05.26.445422: (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
Recombinant DNA Sentences Resources Furthermore, the FoldX AnalyseComplex assay was used for determining the binding affinity between SARS-CoV-2 spike RBD and the ACE2 structurally related receptors ACE, THOP1, and NLN, identified through pGenTHREADER and/or ITASSER analyses. pGenTHREADERsuggested: NoneSoftware and Algorithms Sentences Resources With this aim, the amino acid sequence of ACE2 (NP_001358344.1) was used as query sequence for running pGenThreader (http://bioinf.cs.ucl.ac.uk/psipred/) and I-Tasser (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) to screen the Protein Data Bank (PDB), searching for ACE2 structurally related crystallized proteins [1, 29–35]. http://bioinf.cs.ucl.ac.uk/psipred/suggested: (PSIPRED, RRID:SCR_010246)https://zhanglab.ccmb.med.umich.edu/I-TASSER/suggested: (I-TASSER, RRID:SCR_014627)The variation in the number of interactions (H-bonds, ionic and aromatic interactions) at the SARS-CoV-2 spike RBD/ACE2 interface in presence of the investigated amino acid replacements have been calculated by using the PIC webserver [37] and verified by manual inspection by using PyMOL. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Furthermore, the FoldX AnalyseComplex assay was used for determining the binding affinity between SARS-CoV-2 spike RBD and the ACE2 structurally related receptors ACE, THOP1, and NLN, identified through pGenTHREADER and/or ITASSER analyses. FoldXsuggested: (FoldX, RRID:SCR_008522)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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 8, 16, 19 and 21. 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.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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