Approximate protein structural alignment in polynomial time.

ABSTRACT: 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 epsilon 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 gre

SUBMITTER: Kolodny R 

PROVIDER: S-EPMC514457 | biostudies-literature | 2004 Aug

REPOSITORIES: biostudies-literature