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Protein Science (2002), 11:1575-1579.
Copyright © 2002 The Protein Society

FOR THE RECORD

Fold recognition without folds

Kristin K. Koretke1, Robert B. Russell2,3 and Andrei N. Lupas1,4

1 Microbial Bioinformatics Group, GlaxoSmithKline, Collegeville, Pennsylvania 19426-0989, USA
2 Bioinformatics Research Group, GlaxoSmithKline, Harlow, CM19 5AW, United Kingdom

Reprint requests to: Kristin K. Koretke, GlaxoSmithKline, UP1345, 1250 South Collegeville Road, Collegeville, PA 19426-0989, USA; e-mail: Kristin_K_Koretke{at}sbphrd.com; fax: (610) 917-7901.

Fold recognition predicts protein three-dimensional structure by establishing relationships between a protein sequence and known protein structures. Most methods explicitly use information derived from the secondary and tertiary structure of the templates. Here we show that rigorous application of a sequence search method (PSI-BLAST) with no reference to secondary or tertiary structure information is able to perform as well as traditional fold recognition methods. Since the method, SENSER, does not require knowledge of the three-dimensional structure, it can be used to infer relationships that are not tractable by methods dependent on structural templates.

Keywords: Structure prediction; sequence similarity; fold recognition; PSI-BLAST; HMMer, SENSER


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