Faculty Publications

Structfast: Protein Sequence Remote Homology Detection And Alignment Using Novel Dynamic Programming And Profile-Profile Scoring

Document Type

Article

Keywords

Alignment algorithms, Alignment statistics, Comparative modeling, Homology modeling, Protein structure

Journal/Book/Conference Title

Proteins: Structure, Function and Genetics

Volume

64

Issue

4

First Page

960

Last Page

967

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. © 2006 Wiley-Liss, Inc.

Department

Department of Computer Science

Original Publication Date

9-1-2006

DOI of published version

10.1002/prot.21049

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