title: STRUCTFAST: protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring.
abstract: STRUCTFAST is a novel profile-profile alignment algorithm capable of detecting weak similarities between protein sequences. The increased sensitivity and accuracy of the STRUCTFAST method are achieved through several unique features. First, the algorithm utilizes a novel dynamic programming engine capable of incorporating important information from a structural family directly into the alignment process. Second, the algorithm employs a rigorous analytical formula for profile-profile scoring to overcome the limitations of ad hoc scoring functions that require adjustable parameter training. Third, the algorithm employs Convergent Island Statistics (CIS) to compute the statistical significance of alignment scores independently for each pair of sequences. STRUCTFAST routinely produces alignments that meet or exceed the quality obtained by an expert human homology modeler, as evidenced by its performance in the latest CAFASP4 and CASP6 blind prediction benchmark experiments.
authors.affiliation: Eidogen-Sertanty Inc., San Diego, California 92121, USA.
authors.forename: Derek A
authors.initials: DA
authors.lastname: Debe
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Danzer
authors.forename: William A
authors.initials: WA
authors.lastname: Goddard
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Poleksic
mesh_terms: D000465:Algorithms; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins