Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens

  1. Santrupti Nerli
  2. Nikolaos G. Sgourakis

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  1. Version published to 10.3389/fmedt.2020.553478
  2. ScreenIT

    SciScore for 10.1101/2020.03.23.004176: (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
    SentencesResources
    Identification of SARS-CoV-2 peptide epitopes: The SARS-CoV-2 protein sequences (https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2) were obtained from NCBI and used to generate all possible peptides of lengths 9 and 10 (9,621 9mer and 9,611 10mer peptides).
    NCBI
    suggested: (NCBI, RRID:SCR_006472)
    The website that hosts our database was constructed using the Django web framework.
    Django
    suggested: (Django, RRID:SCR_012855)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    High binding energies can be used as an additional metric to filter low-affinity peptides in the NetMHCpan-4.0 predictions, with the caveat that high energies can be also due to incomplete optimization of the Rosetta energy function as a result of significant deviations between the target and template backbone conformations, not captured by our protocol. We performed 10 independent calculations for each peptide, and the 3 lower-energy models were selected as the final ensemble and used to compute an average binding energy. The results for all 9mer peptides are summarized in Figures 3e, f, while additional results for 10mers are provided through our web-interface and outlined in Supplemental Table 1. As a positive reference, we used the binding energies of the idealized and relaxed PDB templates, which are at a local minimum of the Rosetta scoring function. As a reference set for sub-optimal binders, we modeled decoy structures of poly alanine (polyA) peptide sequences (predicted by NetMHCpan-4.0 to be a top 9th percentile binder for HLA-A*02:01), threaded onto the same PDB templates. We observe a significant, negative (−26 kcal/mol) energy gap between the average binding energies for PDB templates and poly alanine models. The binding energies for all modeled 9mers from the SARS-CoV-2 genome fall between the average energies of the optimal PDB templates and sub-optimal polyA binders, and show a bimodal distribution with significant overlap with the refined PDB template energie...

    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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  3. Version published to 10.1101/2020.03.23.004176v2 on bioRxiv
  4. Version published to 10.1101/2020.03.23.004176v1 on bioRxiv