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Title | Epitome: database of structure-inferred antigenic epitopes. |
Publication Type | Journal Article |
Year of Publication | 2006 |
Authors | Schlessinger, A, Ofran, Y, Yachdav, G, Rost, B |
Journal | Nucleic Acids Res |
Volume | 34 |
Issue | Database issue |
Pagination | D777-80 |
Date Published | 2006 Jan 1 |
ISSN | 1362-4962 |
Keywords | Binding Sites, Antibody, Complementarity Determining Regions, Databases, Protein, Epitopes, B-Lymphocyte, Internet, Models, Molecular, Proteins, User-Computer Interface |
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/. |
DOI | 10.1093/nar/gkj053 |
Alternate Journal | Nucleic Acids Res. |
PubMed ID | 16381978 |
PubMed Central ID | PMC1347416 |
Grant List | R01-GM64633-01 / GM / NIGMS NIH HHS / United States R01-LM07329-01 / LM / NLM NIH HHS / United States |