title: A Cohesive and Integrated Platform for Immunogenicity Prediction.
abstract: In silico methods for immunogenicity prediction mine the enormous quantity of data arising from deciphered genomes and proteomes to identify immunogenic proteins. While high and productive immunogenicity is essential for vaccines, therapeutic proteins and monoclonal antibodies should be minimally immunogenic. Here, we present a cohesive platform for immunogenicity and MHC class I and/or II binding affinity prediction. The platform integrates three quasi-independent modular servers: VaxiJen, EpiJen, and EpiTOP. VaxiJen (http://www.ddg-pharmfac.net/vaxijen) predicts immunogenicity of proteins of different origin; EpiJen (http://www.ddg-pharmfac.net/epijen) predicts peptide binding to MHC class I proteins; and EpiTOP (http://www.ddg-pharmfac.net/epitop) predicts peptide binding to MHC class II proteins. The platform is freely accessible and user-friendly. The protocol for immunogenicity prediction is demonstrated by selecting immunogenic proteins from Mycobacterium tuberculosis and predicting how the peptide epitopes within them bind to MHC class I and class II proteins.
authors.affiliation: School of Pharmacy, Medical University of Sofia, Sofia, 1000, Bulgaria.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dimitrov
authors.affiliation: School of Pharmacy, Medical University of Sofia, Sofia, 1000, Bulgaria.
authors.forename: Mariyana
authors.initials: M
authors.lastname: Atanasova
authors.affiliation: Center for Integrated Protein Science Munich (CIPSM), Technical University of Munich, Freising-Weihenstephan, 85354, Germany.|Department of Life Sciences, Technical University of Munich, Freising-Weihenstephan, 85354, Germany.
authors.forename: Atanas
authors.initials: A
authors.lastname: Patronov
authors.affiliation: School of Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK.
authors.forename: Darren R
authors.initials: DR
authors.lastname: Flower
authors.affiliation: School of Pharmacy, Medical University of Sofia, Sofia, 1000, Bulgaria. idoytchinova@pharmfac.net.
authors.forename: Irini
authors.initials: I
authors.lastname: Doytchinova
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D000939:Epitopes / Q000276:immunology; D015395:Histocompatibility Antigens Class I / Q000276:immunology; D000949:Histocompatibility Antigens Class II / Q000276:immunology; D006801:Humans; D011506:Proteins / Q000276:immunology*
chemical_list: D000939:Epitopes; D015395:Histocompatibility Antigens Class I; D000949:Histocompatibility Antigens Class II; D011506:Proteins
keywords: Immunogenicity; MHC class I binding prediction; MHC class II binding prediction; Proteasome cleavage; TAP binding