In silico design of multi-epitope-based peptide vaccine against SARS-CoV-2 using its spike protein
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
-
-
SciScore for 10.1101/2020.04.23.055467: (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 The three adjuvants were rearranged each time, and the vaccine constructs were analyzed for physicochemical properties using ProtPARAM tool[45], allergenicity[33], antigenicity[32], and scanned for probable stimulants of interferon gamma[36]. ProtPARAMsuggested: (ProtParam Tool, RRID:SCR_018087)The ToxinPred database[35] was used to analyze each of the units of the vaccine construct and hence each of these constructs can be considered nontoxic. 2.8 Molecular Modeling of Vaccine Constructs: The main challenge associated with the molecular modeling of the vaccine constructs was that the … SciScore for 10.1101/2020.04.23.055467: (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 The three adjuvants were rearranged each time, and the vaccine constructs were analyzed for physicochemical properties using ProtPARAM tool[45], allergenicity[33], antigenicity[32], and scanned for probable stimulants of interferon gamma[36]. ProtPARAMsuggested: (ProtParam Tool, RRID:SCR_018087)The ToxinPred database[35] was used to analyze each of the units of the vaccine construct and hence each of these constructs can be considered nontoxic. 2.8 Molecular Modeling of Vaccine Constructs: The main challenge associated with the molecular modeling of the vaccine constructs was that the adjuvant-specific region and the epitope-specific region matched with two different templates. ToxinPredsuggested: (ToxinPred, RRID:SCR_018542)Each of these constructs was then deposited over the GALAXY web server[47] for refinement. GALAXYsuggested: (Galaxy, RRID:SCR_006281)Based on select parameters on which each modeled construct was refined, the best structures were then carried forward for validation through Ramachandran Plot, Z-score over PROCHECK[48] and ProSA-web server[49]. ProSA-websuggested: (ProSA-web, RRID:SCR_018540)Trajectories were analyzed and visualized using GROMACS inbuilt tools and VMD[62]. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Looking into the probable limitations, strategies have been employed to design an epitope-based peptide vaccine utilizing the major subunits of the spike glycoprotein of SARS-CoV-2. In selecting the concerned immunogen, S1 and the S2 domains of the surface glycoprotein have been utilized separately, keeping in mind the limitations associated with using the entire surface glycoprotein[69, 85]. The prediction of the three different types of epitopes (B cells, THTL and TCTL) by utilizing multiple servers in each case based on different algorithms and selection based on a consensus involving all the servers, including experimental basis behind alleles (HLA Class I and Class II), helps add sustenance to the concluded list of epitopes[70–74]. The predicted epitopes were found to be experimentally identified across a recent microarray study of mapped epitopes on the surface glycoprotein [86]. Each of the predicted epitopes was verified based on described parameters and were found to be antigenic, non-allergenic, nontoxic, and share high coverage across the spike glycoprotein of SARS-CoV-2 sequences[37]. The epitope sequences were also matched with a recently deposited SARS-CoV-2 sequence from Gujarat, India (QJC19491.1) and showed complete sequence coverage for all Indian sequences of the spike glycoprotein deposited to date. Based on the necessity of an immunostimulant, an adjuvant’s role becomes important, and specifically, a chimeric adjuvant comprising TLR-4 agonists was designe...
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.
- No funding statement was detected.
- No protocol registration statement was detected.
-
-