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Brutlag, D. L. and Klingler, T. M. (1993). Automatic Discovery of Protein Motifs. In Proceedings of the Ninth International Biotechnology Symposium, Crystal City, Virginia: ACS Books.

Automatic Discovery of Protein Motifs.

D. L. Brutlag & Tod M. Klingler

Department of Biochemistry & Section on Medical Informatics, Stanford University School of Medicine, Stanford, California 94305-5307.

We have developed a novel representation of protein motifs that permits the rapid discovery of structural features in sets of protein sequences with a common structure or function. Many popular methods for representing protein motifs (consensus sequences, weight matrices and profiles) all emphasize conservation of amino acids at specific sites in the sequence. Our method looks for correlations between amino acid residues at distinct sites. Correlations between the residues represent side chain-side chain interactions and give insight into the structural properties of the motifs. Structural correlations can be used in database search to discover other proteins bearing similar relationships. This database search is significantly more sensitive than methods depending only upon conserved residues in protein motifs.

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