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SciScore for 10.1101/2020.04.20.051557: (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 2.1 Protein sequence retrieval: The protein sequences of spike glycoprotein (accession number of QIC53213.1), nucleocapsid phosphoprotein (QHU79211.1), membrane glycoprotein (QIC53207.1) and envelope protein (QIC53215.1) were driven using NCBI (https://www.ncbi.nlm.nih.gov/) databases and saved in FASTA format for subsequent analysis. https://www.ncbi.nlm.nih.gov/suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)2.5 Evaluation of antigenicity: Antigencity of epitopes was assessed by ANTIGENpro (http://scratch.proteomics.ics.uci.edu/) and VaxiJen v2.0 … SciScore for 10.1101/2020.04.20.051557: (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 2.1 Protein sequence retrieval: The protein sequences of spike glycoprotein (accession number of QIC53213.1), nucleocapsid phosphoprotein (QHU79211.1), membrane glycoprotein (QIC53207.1) and envelope protein (QIC53215.1) were driven using NCBI (https://www.ncbi.nlm.nih.gov/) databases and saved in FASTA format for subsequent analysis. https://www.ncbi.nlm.nih.gov/suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)2.5 Evaluation of antigenicity: Antigencity of epitopes was assessed by ANTIGENpro (http://scratch.proteomics.ics.uci.edu/) and VaxiJen v2.0 (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) servers. VaxiJensuggested: (VaxiJen, RRID:SCR_018514)After designing the vaccine, Several physicochemical parameters including molecular weight, theoretical isoelectric point (pI), total number of positive and negative residues, extinction coefficient, Instability index, half-life, aliphatic index, and grand average hydropathy (GRAVY) were computed using Expasy’s ProtParam at http://us.expasy.org/tools/protparam.html [61]. ProtParamsuggested: (ProtParam Tool, RRID:SCR_018087)2.8 Tertiary structure development: The 3-D modeling of designed construct was predicted using the I-TASSER software (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) [61]. I-TASSERsuggested: (I-TASSER, RRID:SCR_014627)The RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php), and ERRAT (http://services.mbi.ucla.edu/ERRAT/) servers were used to validate the refined 3D structures obtained from Galaxy Refine web service. Galaxysuggested: (Galaxy, RRID:SCR_006281)PyMOL is an open-source that widely used for bimolecular function[65]. PyMOLsuggested: (PyMOL, RRID:SCR_000305)The MODELLER program and the Jmol viewer allow the prediction and visualization of immunoepitopes in a given protein sequence or structure. MODELLERsuggested: (MODELLER, RRID:SCR_008395)Next, protein-protein docking of the vaccine structure (as ligand) and each TLR (as receptor) was performed by CLUSPRO 2.0 online server (cluspro.bu.edu/login.php). CLUSPROsuggested: (ClusPro, RRID:SCR_018248)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 32, 35 and 31. 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.
- 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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