title: Broad spectrum assessment of the epitope fluctuation--Immunogenicity hypothesis.
abstract: Prediction of immunogenicity is a substantial barrier in vaccine design. Here, a molecular dynamics approach to assessing the immunogenicity of nanoparticles based on structure is presented. Molecular properties of epitopes on nonenveloped viral particles are quantified via a set of metrics. One such metric, epitope fluctuation (and implied flexibility), is shown to be inversely correlated with immunogenicity for each of a broad spectrum of nonenveloped viruses. The molecular metrics and experimentally determined immunogenicities for these viruses are archived in the open-source vaccine computer-aided design database. Results indicate the promise of computer-aided vaccine design to bring greater efficiency to traditional lab-based vaccine discovery approaches.
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry Indiana University, Bloomington, IN 47405, United States.
authors.forename: Jason S
authors.initials: JS
authors.lastname: Grosch
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry Indiana University, Bloomington, IN 47405, United States.
authors.forename: Jing
authors.initials: J
authors.lastname: Yang
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry Indiana University, Bloomington, IN 47405, United States.
authors.forename: Alice
authors.initials: A
authors.lastname: Shen
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry Indiana University, Bloomington, IN 47405, United States.
authors.forename: Yuriy V
authors.initials: YV
authors.lastname: Sereda
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry Indiana University, Bloomington, IN 47405, United States. Electronic address: ortoleva@indiana.edu.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Ortoleva
mesh_terms: D019295:Computational Biology / Q000379:methods*; D055808:Drug Discovery / Q000379:methods*; D000939:Epitopes / Q000737:chemistry* / Q000276:immunology*; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D053758:Nanoparticles / Q000737:chemistry*; D014765:Viral Vaccines / Q000737:chemistry* / Q000276:immunology*
chemical_list: D000939:Epitopes; D014765:Viral Vaccines
keywords: Bioinformatics; Computer-aided design; Epitope; Immunogenicity; Nanoparticles; Vaccine