title: Statistical significance of threading scores.
abstract: We present a general method for assessing threading score significance. The threading score of a protein sequence, thread onto a given structure, should be compared with the threading score distribution of a random amino-acid sequence, of the same length, thread on the same structure; small p-values point significantly high scores. We claim that, due to general protein contact map properties, this reference distribution is a Weibull extreme value distribution whose parameters depend on the threading method, the structure, the length of the query and the random sequence simulation model used. These parameters can be estimated off-line with simulated sequence samples, for different sequence lengths. They can further be interpolated at the exact length of a query, enabling the quick computation of the p-value.
authors.affiliation: Mathématique, Informatique, et Génome, INRA, Jouy-en-Josas, France.
authors.forename: Afshin Fayyaz
authors.initials: AF
authors.lastname: Movaghar
authors.forename: Guillaume
authors.initials: G
authors.lastname: Launay
authors.forename: Sophie
authors.initials: S
authors.lastname: Schbath
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Gibrat
authors.forename: François
authors.initials: F
authors.lastname: Rodolphe
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D008390:Markov Chains; D015233:Models, Statistical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D016008:Statistical Distributions
chemical_list: D011506:Proteins