RESEARCH ARTICLE


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


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Creative Commons License
© 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


Abstract

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.