Optimizing a widely used protein structure alignment measure in expected polynomial time.

Protein structure alignment is an important tool in many biological applications, such as protein evolution studies, protein structure modeling, and structure-based, computer-aided drug design. Protein structure alignment is also one of the most challenging problems in computational molecular biology, due to an infinite number of possible spatial orientations of any two protein structures. We study one of the most commonly used measures of pairwise protein structure similarity, defined as the number of pairs of atoms in two proteins that can be superimposed under a predefined distance cutoff. We prove that the expected running time of a recently published algorithm for optimizing this (and some other, derived measures of protein structure similarity) is polynomial.