title: A new scoring function and associated statistical significance for structure alignment by CE.
abstract: A new scoring function for assessing the statistical significance of protein structure alignment has been developed. The new scores were tested empirically using the combinatorial extension (CE) algorithm. The significance of a given score was given a p-value by curve-fitting the distribution of the scores generated by a random comparison of proteins taken from the PDB_SELECT database and the structural classification of proteins (SCOP) database. Although the scoring function was developed based on the CE algorithm, it is portable to any other protein structure alignment algorithm. The new scoring function is examined by sensitivity, specificity, and ROC curves.
authors.affiliation: Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA.
authors.forename: Yuting
authors.initials: Y
authors.lastname: Jia
authors.forename: T Gregory
authors.initials: TG
authors.lastname: Dewey
authors.forename: Ilya N
authors.initials: IN
authors.lastname: Shindyalov
authors.forename: Philip E
authors.initials: PE
authors.lastname: Bourne
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software