title: Scan2S: increasing the precision of PROSITE pattern motifs using secondary structure constraints.
abstract: Sequence signature databases such as PROSITE, which include protein pattern motifs indicative of a protein's function, are widely used for function prediction studies, cellular localization annotation, and sequence classification. Correct annotation relies on high precision of the motifs. We present a new and general approach for increasing the precision of established protein pattern motifs by including secondary structure constraints (SSCs). We use Scan2S, the first sequence motif-scanning program to optionally include SSCs, to augment PROSITE pattern motifs. The constraints were derived from either the DSSP secondary structure assignment or the PSIPRED predictions for PROSITE-documented true positive hits. The secondary structure-augmented motifs were scanned against all SwissProt sequences, for which secondary structure predictions were precalculated. Against this dataset, motifs with PSIPRED-derived SSCs exhibited improved performance over motifs with DSSP-derived constraints. The precision of 763 of the 782 PSIPRED-augmented motifs remained unchanged or increased compared to the original motifs; 26 motifs showed an absolute precision increase of 10-30%. We provide the complete set of augmented motifs and the Scan2S program at http://physiology.med.cornell.edu/go/scan2s. Our results suggest a general protocol for increasing the precision of protein pattern detection via the inclusion of SSCs.
authors.affiliation: Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA. las2017@med.cornell.edu
authors.forename: Lucy
authors.initials: L
authors.lastname: Skrabanek
authors.forename: Masha Y
authors.initials: MY
authors.lastname: Niv
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D054834:Lipocalins / Q000737:chemistry; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D054834:Lipocalins