Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2
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SciScore for 10.1101/2020.02.25.965434: (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 Data retrieval and structural analysis: Primary sequence of SARS-CoV-2 protein was retrieved from NCBI database using accession number MN908947.3 [3]. NCBIsuggested: (NCBI, RRID:SCR_006472)Protein sequence was analyzed for its chemicals and physical properties including GRAVY (Grand average of hydropathicity), half-life, molecular weight, stability index and amino acid atomic composition via an online tool Protparam [13] Protparamsuggested: (ProtParam Tool, RRID:SCR_018087)TMHMM v2.0 (http://www.cbs.dtu.dk/services/TMHMM/) was applied to examine the transmembrane topology of S protein. http:/…SciScore for 10.1101/2020.02.25.965434: (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 Data retrieval and structural analysis: Primary sequence of SARS-CoV-2 protein was retrieved from NCBI database using accession number MN908947.3 [3]. NCBIsuggested: (NCBI, RRID:SCR_006472)Protein sequence was analyzed for its chemicals and physical properties including GRAVY (Grand average of hydropathicity), half-life, molecular weight, stability index and amino acid atomic composition via an online tool Protparam [13] Protparamsuggested: (ProtParam Tool, RRID:SCR_018087)TMHMM v2.0 (http://www.cbs.dtu.dk/services/TMHMM/) was applied to examine the transmembrane topology of S protein. http://www.cbs.dtu.dk/services/TMHMM/suggested: (TMHMM Server, RRID:SCR_014935)Existence of disulphide-bonds were examined through an online tool DIANNA v1.1 which uses trained neural system to make predictions [15]. DIANNAsuggested: (DiANNA, RRID:SCR_018529)Pymol was used to examine the positions of selected linear and discontinuous epitopes on the 3D structure of SARS-CoV-2 protein. Pymolsuggested: (PyMOL, RRID:SCR_000305)The antigenicity score of each epitope was calculated by VaxiJen v2.0. VaxiJensuggested: (VaxiJen, RRID:SCR_018514)The phylogenetic tree of the S proteins with mutations were generated using MEGA software [23]. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)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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