An Attempt to Improve the Quantitative Epitope Prediction by Modelling Alternative Binding Modes
Aluffi-Pentini Filippo1, VFonzo aleria De2, Parisi Valerio*, 2
Identifiers and Pagination:Year: 2009
First Page: 51
Last Page: 58
Publisher ID: TOBIOIJ-3-51
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
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.
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.
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.