An Attempt to Improve the Quantitative Epitope Prediction by Modelling Alternative Binding Modes

Filippo, Aluffi-Pentini; aleria De, VFonzo; Valerio, Parisi

An Attempt to Improve the Quantitative Epitope Prediction by Modelling Alternative Binding Modes

Aluffi-Pentini Filippo¹, VFonzo aleria De², Parisi Valerio^{*, 2}

¹ Dipartimento Metodi e Modelli Matematici, Università di Roma “La Sapienza”, Via A. Scarpa 16, 00161 Roma, Italy

² Dipartimento di Medicina Sperimentale, Università di Roma “La Sapienza”, Viale Regina Elena 324, 00161 Roma, Italy

Article Information

Identifiers and Pagination:

Year: 2009
Volume: 3
First Page: 51
Last Page: 58
Publisher ID: TOBIOIJ-3-51
DOI: 10.2174/1875036200903010051

Article History:

Received Date: 15/06/2009
Revision Received Date: 01/08/2009
Acceptance Date: 04/08/2009
Electronic publication date: 18/09/2009
Collection year: 2009

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© 2009 Filippo et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

^* Address correspondence to this author at the Dipartimento di Medicina Sperimentale, Università di Roma “La Sapienza”, Viale Regina Elena 324, 00161 Roma, Italy; Tel: +39 06 4991 0774; Fax: +39 338 0 9981736; E-mail: valerio.parisi@uniroma1.it

Motivation:

A good quantitative epitope prediction, i.e. a reliable prediction of the strength of the MHC-epitope binding, is decisive in order to better understand the immune system response. The prediction is often performed by means of the scoring-matrix method that usually assumes a single binding configuration: each amino acid of the epitope binds to a specific pocket of the MHC molecule, in a way independent from other bindings.

Results:

We have put forward the assumption, suggested by the allosteric Monod framework, that a number of alternative states exist, each one characterised by an interaction energy expressed by a scoring matrix. We have developed and suitably evaluated an algorithm for epitope prediction based on such assumption, and we finally discuss the results and the possible reasons why such results unexpectedly appear to be unsatisfactory.

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RESEARCH ARTICLE

An Attempt to Improve the Quantitative Epitope Prediction by Modelling Alternative Binding Modes

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