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Protein Science (2004), 13:1841-1850. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Database searching by flexible protein structure alignment

Yuzhen Ye and Adam Godzik

The Burnham Institute, La Jolla, California 92037, USA

(RECEIVED December 23, 2003; FINAL REVISION March 27, 2004; ACCEPTED March 29, 2004)



Abstract

We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures. One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases. However, none of the flexible structure alignment methods were applied in this task because of a lack of significance estimation of flexible alignments. In this paper, we developed an estimate of the statistical significance of FATCAT alignment score, allowing us to use it as a database-searching tool. The results reported here show that (1) the distribution of the similarity score of FATCAT alignment between two unrelated protein structures follows the extreme value distribution (EVD), adding one more example to the current collection of EVDs of sequence and structure similarities; (2) introducing flexibility into structure comparison only slightly influences the sensitivity and specificity of identifying similar structures; and (3) the overall performance of FATCAT as a database searching tool is comparable to that of the widely used rigid-body structure comparison programs DALI and CE. Two examples illustrating the advantages of using flexible structure alignments in database searching are also presented. The conformational flexibilities that were detected in the first example may be involved with substrate specificity, and the conformational flexibilities detected in the second example may reflect the evolution of structures by block building.

Keywords: flexible structure comparison; significance analysis; structural database search

Reprint requests to: Yuzhen Ye or Adam Godzik, Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA; e-mail: yye{at}burnham.org or adam{at}burnham.org; fax: (858) 646-3171.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03602304.

Supplemental material: see http://fatcat.burnham.org


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