Summary: Trust Region Superposition Methods for Protein Alignment
J. M. Mart´inez
L. Mart´inez §
June 7, 2007
Protein Alignment is a challenging applied Optimization problem. Superposition meth-
ods are based on the maximization of a score function with respect to rigid-body modi-
fications 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
Proteins are large organic compounds formed by chains of -amino acids bound by peptide
bonds. They are essential parts of all living organisms and participate in most cellular processes.
Hormone recognition and transport, catalysis, transcription regulation, photosynthesis, cellular
respiration, and many other fundamental mechanisms of life are protein-mediated. Proteins can
work together to achieve a particular function, and can bind to different chemical structures to