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IMA Journal of Numerical Analysis Advance Access published online on May 2, 2008
IMA Journal of Numerical Analysis, doi:10.1093/imanum/drn012
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© The author 2008. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

Trust-region superposition methods for protein alignment

R. Andreani{dagger} and J. M. Martínez{ddagger}

Department of Applied Mathematics, IMECC-UNICAMP, State University of Campinas, CP 6065, 13081-970 Campinas SP, Brazil

L. Martínez§

Institute of Chemistry, State University of Campinas, SP, Brazil and Institut Pasteur, Paris, France

{dagger} Email: andreani{at}ime.unicamp.br

{ddagger} Corresponding author. Email: martinez{at}ime.unicamp.br

§ Email: lmartinez{at}iqm.unicamp.br

Received on 31 January 2007. Accepted for publication 1 February 2008.


  Abstract

Protein alignment is a challenging applied optimization problem. Superposition methods are based on the maximization of a score function with respect to rigid-body modifications of relative positions. The problem of score maximization can be modelled as a continuous nonsmooth optimization problem (low order-value optimization (LOVO)). This allows one to define practical and convergent methods that produce monotone increases of the score. In this paper, trust-region methods are introduced for solving the problem. Numerical results are presented. Computer software related to the LOVO approach for protein alignment is available at www.ime.unicamp.br/ ~ martinez/lovoalign.

Key Words: protein alignment; trust-region methods; low order-value optimization

This work is dedicated to the 70th birthday of Prof. M. J. D. Powell in September 2006.


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