title: Epitome: database of structure-inferred antigenic epitopes.
abstract: Immunoglobulin molecules specifically recognize particular areas on the surface of proteins. These areas are commonly dubbed B-cell epitopes. The identification of epitopes in proteins is important both for the design of experiments and vaccines. Additionally, the interactions between epitopes and antibodies have often served as a model for protein-protein interactions. One of the main obstacles in creating a database of antigen-antibody interactions is the difficulty in distinguishing between antigenic and non-antigenic interactions. Antigenic interactions involve specific recognition sites on the antibody's surface, while non-antigenic interactions are between a protein and any other site on the antibody. To solve this problem, we performed a comparative analysis of all protein-antibody complexes for which structures have been experimentally determined. Additionally, we developed a semi-automated tool that identified the antigenic interactions within the known antigen-antibody complex structures. We compiled those interactions into Epitome, a database of structure-inferred antigenic residues in proteins. Epitome consists of all known antigen/antibody complex structures, a detailed description of the residues that are involved in the interactions, and their sequence/structure environments. Interactions can be visualized using an interface to Jmol. The database is available at http://www.rostlab.org/services/epitome/.
authors.affiliation: CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, room 804, New York, NY 10032, USA. as2067@columbia.edu
authors.forename: Avner
authors.initials: A
authors.lastname: Schlessinger
authors.forename: Yanay
authors.initials: Y
authors.lastname: Ofran
authors.forename: Guy
authors.initials: G
authors.lastname: Yachdav
authors.forename: Burkhard
authors.initials: B
authors.lastname: Rost
mesh_terms: D001666:Binding Sites, Antibody; D022801:Complementarity Determining Regions / Q000737:chemistry* / Q000276:immunology; D030562:Databases, Protein; D018985:Epitopes, B-Lymphocyte / Q000737:chemistry* / Q000276:immunology; D020407:Internet; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry / Q000276:immunology*; D014584:User-Computer Interface
chemical_list: D022801:Complementarity Determining Regions; D018985:Epitopes, B-Lymphocyte; D011506:Proteins