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Protein Science (2005), 14:1305-1314. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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Structural similarity to bridge sequence space: Finding new families on the bridges

Parantu K. Shah1,2, Patrick Aloy1, Peer Bork1,2 and Robert B. Russell1

1 EMBL, 69117 Heidelberg, Germany2 Max Delbruck Center for Molecular Medicine, 13125 Berlin-Buch, Germany

(RECEIVED October 21, 2004; FINAL REVISION February 1, 2005; ACCEPTED February 1, 2005)

Structures for protein domains have increased rapidly in recent years owing to advances in structural biology and structural genomics projects. New structures are often similar to those solved previously, and such similarities can give insights into function by linking poorly understood families to those that are better characterized. They also allow the possibility of combing information to find still more proteins adopting a similar structure and sometimes a similar function, and to reprioritize families in structural genomics pipelines. We explore this possibility here by preparing merged profiles for pairs of structurally similar, but not necessarily sequence-similar, domains within the SMART and Pfam database by way of the Structural Classification of Proteins (SCOP). We show that such profiles are often able to successfully identify further members of the same superfamily and thus can be used to increase the sensitivity of database searching methods like HMMer and PSI-BLAST. We perform detailed benchmarks using the SMART and Pfam databases with four complete genomes frequently used as annotation benchmarks. We quantify the associated increase in structural information in Swissprot and discuss examples illustrating the applicability of this approach to understand functional and evolutionary relationships between protein families.

Keywords: structural genomics; protein structure; domain family; evolution

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041187405.

Reprint requests to: Robert B. Russell, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany; e-mail: russell{at}embl.de; fax: +49-6221-387517.


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