title: Fold recognition without folds.
abstract: Fold recognition predicts protein three-dimensional structure by establishing relationships between a protein sequence and known protein structures. Most methods explicitly use information derived from the secondary and tertiary structure of the templates. Here we show that rigorous application of a sequence search method (PSI-BLAST) with no reference to secondary or tertiary structure information is able to perform as well as traditional fold recognition methods. Since the method, SENSER, does not require knowledge of the three-dimensional structure, it can be used to infer relationships that are not tractable by methods dependent on structural templates.
authors.affiliation: Microbial Bioinformatics Group, GlaxoSmithKline, Collegeville, Pennsylvania 19426-0989, USA. Kristin_K_Koretke@sbphrd.com
authors.forename: Kristin K
authors.initials: KK
authors.lastname: Koretke
authors.forename: Robert B
authors.initials: RB
authors.lastname: Russell
authors.forename: Andrei N
authors.initials: AN
authors.lastname: Lupas
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D011506:Proteins