title: Optimizing energy potential for protein fold recognition with parametric evaluation function.
abstract: In this paper, a new optimization method is proposed to determine a simplified energy potential for protein fold recognition, which consists of the residue-residue contact, hydrophobicity, and pseudodihedral potentials. With a parametric evaluation function method, the Z-scores of all the proteins in a training set are optimized simultaneously to obtain the best parameter set of the potential. For this multi-objective and multi-constraint problem, the new optimization scheme is very effective. The derived potential is then tested on two high-quality decoy sets and compared with other classical fold recognition potentials. With the simplified energy potential, we achieve a high level of discrimination capability between correct and incorrect folds.
authors.affiliation: Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, China.
authors.forename: Junfeng
authors.initials: J
authors.lastname: Gu
authors.forename: Honglin
authors.initials: H
authors.lastname: Li
authors.forename: Hualiang
authors.initials: H
authors.lastname: Jiang
authors.forename: Xicheng
authors.initials: X
authors.lastname: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D011506:Proteins