Trust Region Superposition Methods for Protein Alignment

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 modeled as a continuous nonsmooth optimization problem (LOVO). This allows one to define practical and convergent methods that produce monotone increase 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 in www.ime.unicamp.br/∼martinez/lovoalign