A gold standard set of mechanistically diverse enzyme superfamilies

Genome Biology
Shoshana D BrownPatricia C Babbitt

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.

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Methods Mentioned

BETA
X-ray

Software Mentioned

HMMPFAM
SUPERFAMILY
PSI
Pfam
Fasta
BLAST

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