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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2006

Open Access Research

The MEPS server for identifying protein conformational epitopes

Tiziana Castrignanò1, Paolo D'Onorio De Meo1, Danilo Carrabino1, Massimilano Orsini2, Matteo Floris2 and Anna Tramontano234*

Author Affiliations

1 CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita' e Ricerca, Via dei Tizii, 6/b, 5 I-00185 Rome, Italy

2 Center for Advanced Studies, Research and Development in Sardinia (CRS4), Bioinformatics Unit, Parco Scientifico e Tecnologico, POLARIS, Edificio 1, 09010 PULA (CA), Italy

3 Department of Biochemical Sciences, University 'La Sapienza', P.le Aldo Moro, 5, I-00185 Rome, Italy

4 Istituto Pasteur – Fondazione Cenci Bolognetti, University 'La Sapienza', P.le Aldo Moro, 5, I-00185 Rome, Italy

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BMC Bioinformatics 2007, 8(Suppl 1):S6  doi:10.1186/1471-2105-8-S1-S6

Published: 8 March 2007

Abstract

Background

One of the most interesting problems in molecular immunology is epitope mapping, i.e. the identification of the regions of interaction between an antigen and an antibody. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues involved in the interaction and could be instrumental both in designing peptides able to mimic the interacting surface of the antigen and in understanding where immunologically important regions are located in its three-dimensional structure. From an experimental point of view, both genetically encoded and chemically synthesised peptide libraries can be used to identify sequences recognized by a given antibody. The problem then arises of which region of a folded protein the selected peptides correspond to.

Results

We have developed a method able to find the surface region of a protein that can be effectively mimicked by a peptide, given the structure of the protein and the maximum number of side chains deemed to be required for recognition. The method is implemented as a publicly available server. It can also find and report all peptide sequences of a specified length that can mimic the surface of a given protein and store them in a database.

The immediate application of the server is the mapping of antibody epitopes, however the system is sufficiently flexible for allowing other questions to be asked, for example one can compare the peptides representing the surface of two proteins known to interact with the same macromolecule to find which is the most likely interacting region.

Conclusion

We believe that the MEPS server, available at http://www.caspur.it/meps webcite, will be a useful tool for immunologists and structural and computational biologists. We plan to use it ourselves to implement a database of "surface mimicking peptides" for all proteins of known structure and proteins that can be reliably modelled by comparative modelling.