Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering
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SciScore for 10.1101/2020.08.14.251496: (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 For each 15-mer, the T cell MHC-II promiscuous epitopes were predicted using NetMHCIIpan v3.2 [33], and an epitope was counted if the median percentile rank was ≤ 20.0% by binding the 15-mer to any of the seven MHC-II alleles [34] (i.e., HLA-DRB1*03:01, HLA-DRB1*07:01, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, and HLA-DRB5*01:01). NetMHCIIpansuggested: NoneThe conserved epitopes were determined by the IEDB epitope clustering tool [38] and aligned using SEAVIEW [39]. SEAVIEWsuggested: (SeaView, RRID:SCR_015059)The ectodomain of the S homotrimers was visualized via PyMOL … SciScore for 10.1101/2020.08.14.251496: (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 For each 15-mer, the T cell MHC-II promiscuous epitopes were predicted using NetMHCIIpan v3.2 [33], and an epitope was counted if the median percentile rank was ≤ 20.0% by binding the 15-mer to any of the seven MHC-II alleles [34] (i.e., HLA-DRB1*03:01, HLA-DRB1*07:01, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, and HLA-DRB5*01:01). NetMHCIIpansuggested: NoneThe conserved epitopes were determined by the IEDB epitope clustering tool [38] and aligned using SEAVIEW [39]. SEAVIEWsuggested: (SeaView, RRID:SCR_015059)The ectodomain of the S homotrimers was visualized via PyMOL [43]. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:However, a major limitation of the present study is the wet-lab experimental validation of the designed proteins. First, the newly designed protein sequences need to be folded properly with a structure comparable to that of the native S protein. Second, the capability of the newly added epitopes for binding MHC-II molecules and subsequently inducing immune responses need to be validated. Finally, these candidates should be tested for their protectiveness and safety in animal models. Overall, this study presents a strategy to improve the immunogenicity and antigenicity of a vaccine candidate by manipulating the MHC-II T cell epitopes through computational protein design. In the current settings, the immunogenicity evaluation was carried out after the standard protein design simulations with EvoDesign. In the future, the assessment of the immunogenic potential could be incorporated into the protein design process so that the sequence decoy generated at each step will be guided by balancing both the protein stability and immunogenicity. Moreover, with proper prior knowledge of known epitopes (e.g., both MHC-I and MHC-II from the pathogen proteome), it is also possible to create a chimeric protein, which integrates epitopes from antigens other than the target protein.
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04456595 Active, not recruiting Clinical Trial of Efficacy and Safety of Sinovac's Adsorbed … 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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