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Bioinformatics Advance Access originally published online on April 8, 2004
Bioinformatics 2004 20(15):2380-2389; doi:10.1093/bioinformatics/bth255
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Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.

Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families

Ricardo Núñez Miguel

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom

Received on December 18, 2003; accepted on March 12, 2004
Advance Access Publication April 8, 2004

Motivation: Most proteins have evolved to perform specific functions that are dependent on the adoption of well-defined three-dimensional (3D) structures. Specific patterns of conserved residues in amino acid sequences of divergently evolved proteins are frequently observed; these may reflect evolutionary restraints arising both from the need to maintain tertiary structure and the requirement to conserve residues more directly involved in function. Databases of such sequence patterns are valuable in identifying distant homologues, in predicting function and in the study of evolution.

Results: A fully automated database of protein sequence patterns, Functional Protein Sequence Pattern Database (FPSPD), has been derived from the analysis of the conserved residues that are predicted to be functional in structurally aligned homologous families in the HOMSTRAD database. Environment-dependent substitution tables, evolutionary trace analysis, solvent accessibility calculations and 3D-structures were used to obtain the FPSPD. The method yielded 3584 patterns that are considered functional and 3049 patterns that are probably functional. FPSPD could be useful for assigning a protein to a homologous superfamily and thereby providing clues about function.

Availability: FPSPD is available at http://www-cryst.bioc.cam.ac.uk/~fpspd/

Contact: Ricardo{at}cryst.bioc.cam.ac.uk


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