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Open Access Method

A gold standard set of mechanistically diverse enzyme superfamilies

Shoshana D Brown1, John A Gerlt2, Jennifer L Seffernick3 and Patricia C Babbitt4*

Author Affiliations

1 Department of Biopharmaceutical Sciences, University of California, 1700 4th Street, San Francisco, San Francisco, CA 94143-2550, USA

2 Department of Biochemistry, University of Illinois, Roger Adams Laboratory, 600 S Mathews Avenue, Urbana, IL 61801, USA

3 Department of Biochemistry, Molecular Biology, and Biophysics, Biological Process Technology Institute, and Center for Microbial and Plant Genomics, University of Minnesota, St Paul, MN 55108, USA

4 Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, 1700 4th Street, San Francisco, San Francisco, CA 94143-2550, USA

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Genome Biology 2006, 7:R8  doi:10.1186/gb-2006-7-1-r8

Published: 31 January 2006

Abstract

Superfamily and family analyses provide an effective tool for the functional classification of proteins, but must be automated for use on large datasets. We describe a 'gold standard' set of enzyme superfamilies, clustered according to specific sequence, structure, and functional criteria, for use in the validation of family and superfamily clustering methods. The gold standard set represents four fold classes and differing clustering difficulties, and includes five superfamilies, 91 families, 4,887 sequences and 282 structures.