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Protein Engineering, Vol. 14, No. 7, 455-458, July 2001
© 2001 Oxford University Press

COMMUNICATION

Sequence-based detection of distantly related proteins with the same fold

Igor V. Grigoriev1, Chao Zhang and Sung-Hou Kim,2

Department of Chemistry and E. O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA 1 Present address: Sugen Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA


   Introduction
 
Because proteins that have diverged beyond significant sequence similarity still retain the three-dimensional (3D) fold of their ancestor (Chothia and Lesk, 1986Go; Rost, 1997Go), the recognition of structural similarity between proteins provides powerful clues to ancestry. In fact, a large number of distant homology relationships were identified only after the structures of the proteins had been solved (Murzin, 1998Go). However, structures are being determined only for a small fraction of the proteins. There is a pressing need for improvement in the performance of sequence-based methods for the detection of proteins with the same fold but scant sequence similarity. Here, we examine how to achieve this goal by combining three kinds of information from a protein sequence.

First, it has long been recognized that the use of multiply-aligned sequences from a protein family improves the sensitivity of homology detection. This idea is used by many recent computational procedures . . . [Full Text of this Article]


   Methods
 
The benchmark

Compatibility functions

Alignment and scoring


   Results
 

   Discussion
 

   Notes
 

   Acknowledgments
 

   References
 

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