Epitome: database of structure-inferred antigenic epitopes.

TitleEpitome: database of structure-inferred antigenic epitopes.
Publication TypeJournal Article
Year of Publication2006
AuthorsSchlessinger, A, Ofran, Y, Yachdav, G, Rost, B
JournalNucleic Acids Res
IssueDatabase issue
Date Published2006 Jan 1
KeywordsBinding Sites, Antibody, Complementarity Determining Regions, Databases, Protein, Epitopes, B-Lymphocyte, Internet, Models, Molecular, Proteins, User-Computer Interface

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/.

Alternate JournalNucleic Acids Res.
PubMed ID16381978
PubMed Central IDPMC1347416
Grant ListR01-GM64633-01 / GM / NIGMS NIH HHS / United States
R01-LM07329-01 / LM / NLM NIH HHS / United States