Algorithmic aspects of protein structure similarity

Abstract

We show that calculating contact map overlap (a measure of similarity of protein structures) is NP-hard, but can be solved in polynomial time for several interesting and relevant special cases. We identify an important special case of this problem corresponding to self-avoiding walks, and prove a decomposition theorem and a corollary approximation result for this special case. These are the first approximation algorithms with guaranteed error bounds, and NP-completeness results in the literature in the area of protein structure alignment/fold recognition for measures of structure similarity of practical interest.