title: Designing string-of-beads vaccines with optimal spacers.
abstract: String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial.We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44% compared to designs without spacers.
authors.affiliation: Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany. schubert@informatik.uni-tuebingen.de.|Department of Computer Science, Applied Bioinformatics, 72076, Tübingen, Germany. schubert@informatik.uni-tuebingen.de.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Schubert
authors.affiliation: Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany. oliver.kohlbacher@uni-tuebingen.de.|Department of Computer Science, Applied Bioinformatics, 72076, Tübingen, Germany. oliver.kohlbacher@uni-tuebingen.de.|Quantitative Biology Center, 72076, Tübingen, Germany. oliver.kohlbacher@uni-tuebingen.de.|Faculty of Medicine, University of Tübingen, 72076, Tübingen, Germany. oliver.kohlbacher@uni-tuebingen.de.
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
mesh_terms: D000465:Algorithms; D021901:DNA, Intergenic; D000939:Epitopes / Q000235:genetics / Q000276:immunology*; D005805:Genes, MHC Class I; D006801:Humans; D008957:Models, Genetic; D018448:Models, Immunological; D019444:Vaccines, DNA / Q000235:genetics* / Q000276:immunology
chemical_list: D021901:DNA, Intergenic; D000939:Epitopes; D019444:Vaccines, DNA
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