title: A gold standard set of mechanistically diverse enzyme superfamilies.
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.
authors.affiliation: Department of Biopharmaceutical Sciences, University of California, 1700 4th Street, San Francisco, San Francisco, CA 94143-2550, USA.
authors.forename: Shoshana D
authors.initials: SD
authors.lastname: Brown
authors.forename: John A
authors.initials: JA
authors.lastname: Gerlt
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Seffernick
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Babbitt
mesh_terms: D017124:Conserved Sequence; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry* / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D005810:Multigene Family / Q000235:genetics*; D015203:Reproducibility of Results; D040681:Structural Homology, Protein
chemical_list: D004798:Enzymes