In silico Design and Characterization of Multi-epitopes Vaccine for SARS-CoV2 from Its Spike Protein
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SciScore for 10.1101/2020.06.03.131755: (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 Selection of protein for epitope prediction: Complete Spike protein sequence (P0DTC2) of SARS-CoV2 was downloaded in fasta format from UniProt protein database. UniProtsuggested: (UniProtKB, RRID:SCR_004426)Antigenicity of epitopes was analyzed by online server VaxiJen v2.0 (http://www.ddg-harmfac.net/vaxijen/VaxiJen/VaxiJen.html). VaxiJensuggested: (VaxiJen, RRID:SCR_018514)AllerTop v2.0 and AllergenFP were two online tools utilized for the prediction of allergenicity of chimeric protein. AllerTopsuggested: (AllerTop, RRID:SCR_018496)PROSO II server works on an approach of classifier which … SciScore for 10.1101/2020.06.03.131755: (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 Selection of protein for epitope prediction: Complete Spike protein sequence (P0DTC2) of SARS-CoV2 was downloaded in fasta format from UniProt protein database. UniProtsuggested: (UniProtKB, RRID:SCR_004426)Antigenicity of epitopes was analyzed by online server VaxiJen v2.0 (http://www.ddg-harmfac.net/vaxijen/VaxiJen/VaxiJen.html). VaxiJensuggested: (VaxiJen, RRID:SCR_018514)AllerTop v2.0 and AllergenFP were two online tools utilized for the prediction of allergenicity of chimeric protein. AllerTopsuggested: (AllerTop, RRID:SCR_018496)PROSO II server works on an approach of classifier which utilizes difference between TargetDB and PDB and insoluble proteins of TargetDB. TargetDBsuggested: NonePSIPRED 3.2 attains average Q3 score of 81.6% obtained using very stringent cross approval strategies to assess its performance. PSIPREDsuggested: (PSIPRED, RRID:SCR_010246)Tertiary structure of multi-epitopes chimeric vaccine candidate was built using I TASSER online server (https://zhanglab.ccmb.med.umich.edu/I-TASSER/). https://zhanglab.ccmb.med.umich.edu/I-TASSER/suggested: (I-TASSER, RRID:SCR_014627)Structure refined by Galaxy server of best quality in accordance with community-wide CASP10 experiments(58). Galaxysuggested: (Galaxy, RRID:SCR_006281)ProSA-web (https://prosa.services.came.sbg.ac.at/prosa.php), The ERRAT server (http://services.mbi.ucla.edu/ERRAT/) and RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) web servers were utilized for 3D structure validation obtained after galaxy server refinement(59) RAMPAGEsuggested: (RAMPAGE, RRID:SCR_017590)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: 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.
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