title: Performance of threading scoring functions designed using new optimization method.
abstract: We present a new procedure for optimization of a threading scoring function. A scoring function is usually formulated in terms of the structural environment states that describe the protein fold model. We propose a method for the optimal selection of those structural environment states that naturally follows from the probabilistic description of the threading problem and is done prior to threading experiments. We demonstrate the selection of the optimal structural environment states for the solvent exposure of the amino acid position, and present the results of threading experiments performed using scoring functions designed with and without the optimization of the structural environment states. These results confirm that the optimal scoring function predicts the sequence-to-structure alignments most accurately. Threading experiments performed with 15 optimally designed scoring functions show that the correlation coefficient between the information content of the amino acid distribution that determines the scoring function and the accuracy of the optimal sequence-to-structure alignment is 0.94.
authors.affiliation: BioMolecular Engineering Research Center, College of Engineering, Boston University, Massachusetts 02215, USA. jadwiga@darwin.bu.edu
authors.forename: J R
authors.initials: JR
authors.lastname: Bieńkowska
authors.forename: R G
authors.initials: RG
authors.lastname: Rogers
authors.forename: T F
authors.initials: TF
authors.lastname: Smith
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D015233:Models, Statistical; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D012997:Solvents
chemical_list: D000596:Amino Acids; D011506:Proteins; D012997:Solvents