Scrutinizing the SARS-CoV-2 protein information for designing an effective vaccine encompassing both the T-cell and B-cell epitopes
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SciScore for 10.1101/2020.03.26.009209: (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 Firstly, the antigenic proteins were analyzed by using NetMHCIIPan 3.2 server (http://www.cbs.dtu.dk/services/NetMHCIIpan/) [34]. NetMHCIIPansuggested: NoneThe structures of the SARS-CoV-2 proteins were constructed using I-TASSER (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) [43]and HTL and CTL epitopes were mapped and their structures were retrieved using PyMol tool. I-TASSERsuggested: (I-TASSER, RRID:SCR_014627)PyMolsuggested: (PyMOL, RRID:SCR_000305)The predicted epitopes were checked for their antigenicity using VaxiJen server, allergenicity by using AlgPred and toxicity by ToxinPred … SciScore for 10.1101/2020.03.26.009209: (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 Firstly, the antigenic proteins were analyzed by using NetMHCIIPan 3.2 server (http://www.cbs.dtu.dk/services/NetMHCIIpan/) [34]. NetMHCIIPansuggested: NoneThe structures of the SARS-CoV-2 proteins were constructed using I-TASSER (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) [43]and HTL and CTL epitopes were mapped and their structures were retrieved using PyMol tool. I-TASSERsuggested: (I-TASSER, RRID:SCR_014627)PyMolsuggested: (PyMOL, RRID:SCR_000305)The predicted epitopes were checked for their antigenicity using VaxiJen server, allergenicity by using AlgPred and toxicity by ToxinPred server. 9. VaxiJensuggested: (VaxiJen, RRID:SCR_018514)Solubility of the construct was calculated using SolPro tool available at SCRATCH protein predictor server (http://scratch.proteomics.ics.uci.edu/) [49]. SolProsuggested: NoneSCRATCHsuggested: (SCRATCH, RRID:SCR_014291)Vaccine construct structure prediction and validation: Secondary structure of the multi-epitope vaccine construct was predicted using SOPMA(https://npsa-prabi.ibcp.fr/cgibin/npsa_automat.pl?page=/NPSA/npsa_sopma.html) [50] and PSI-PRED (http://bioinf.cs.ucl.ac.uk/psipred/) server [51]. http://bioinf.cs.ucl.ac.uk/psipred/suggested: (PSIPRED, RRID:SCR_010246)The structures were evaluated by constructing Ramachandran plot using RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) and the quality was assessed using ERRAT server (https://servicesn.mbi.ucla.edu/ERRAT/). 14. RAMPAGEsuggested: (RAMPAGE, RRID:SCR_017590)Standard molecular dynamics of the vaccine construct: The refined modelled structure of the multi-epitope vaccine construct was further evaluated for its stability in the real environment by simulating it in a water sphere using NAMD-standard molecular dynamics tool (https://www.ks.uiuc.edu/Research/namd/) by using parallel processors. https://www.ks.uiuc.edu/Research/namd/suggested: (NAMD, RRID:SCR_014894)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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32, 33 and 29. 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:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- No funding statement was detected.
- No protocol registration statement was detected.
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