Skip Navigation

Nucleic Acids Research 2006 34(Database Issue):D777-D780; doi:10.1093/nar/gkj053
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1409K) Freely available
Right arrow Screen PDF (219K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Schlessinger, A.
Right arrow Articles by Rost, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schlessinger, A.
Right arrow Articles by Rost, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2006, Vol. 34, Database issue D777-D780
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Epitome: database of structure-inferred antigenic epitopes

Avner Schlessinger1,2,3,*, Yanay Ofran1,2, Guy Yachdav1,2,3 and Burkhard Rost1,2,3

1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University 1130 St Nicholas Avenue room 804, New York, NY 10032, USA 2Columbia University Center for Computational Biology and Bioinformatics (C2B2) 1130 St Nicholas Avenue room 804, New York, NY 10032, USA 3NorthEast Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University 1130 St. Nicholas Avenue room 804, New York, NY 10032, USA

*To whom correspondence should be addressed. Tel: +1 212 851 4669; Fax: +1 212 305 7932; Email: as2067{at}columbia.edu

Received August 15, 2005. Revised September 23, 2005. Accepted October 4, 2005.

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/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
M. J. Sweredoski and P. Baldi
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure
Bioinformatics, June 15, 2008; 24(12): 1459 - 1460.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Gunther, D. Hempel, M. Dunkel, K. Rother, and R. Preissner
SuperHapten: a comprehensive database for small immunogenic compounds
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D906 - D910.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
P. Haste Andersen, M. Nielsen, and O. Lund
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
Protein Sci., November 1, 2006; 15(11): 2558 - 2567.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.