Approximate protein structural alignment in polynomial time

Alignment of protein structures is a fundamental task in computational molecular biology. Good structural alignments can help detect distant evolutionary relationships that are hard or impossible to discern from protein sequences alone. Here, we study the structural alignment problem as a family of optimization problems and develop an approximate polynomial-time algorithm to solve them. For a commonly used scoring function, the algorithm runs in O(n(10)/epsilon(6)) time, for globular protein of length n, and it detects alignments that score within an additive error of E from all optima. Thus, we prove that this task is computationally feasible, although the method that we introduce is too slow to be a useful everyday tool. We argue that such approximate solutions are, in fact, of greater interest than exact ones because of the noisy nature of experimentally determined protein coordinates. The measurement of similarity between a pair of protein structures used by our algorithm involves the Euclidean distance between the structures (appropriately rigidly transformed). We show that an alternative approach, which relies on internal distance matrices, must incorporate sophisticated geometric ingredients if it is to guarantee optimality and run in polynomial time. We use these observations to visualize the scoring function for several real instances of the problem. Our investigations yield insights on the computational complexity of protein alignment under various scoring functions. These insights can be used in the design of scoring functions for which the optimum can be approximated efficiently and perhaps in the development of efficient algorithms for the multiple structural alignment problem.