title: Local quality assessment in homology models using statistical potentials and support vector machines.
abstract: In this study, we address the problem of local quality assessment in homology models. As a prerequisite for the evaluation of methods for predicting local model quality, we first examine the problem of measuring local structural similarities between a model and the corresponding native structure. Several local geometric similarity measures are evaluated. Two methods based on structural superposition are found to best reproduce local model quality assessments by human experts. We then examine the performance of state-of-the-art statistical potentials in predicting local model quality on three qualitatively distinct data sets. The best statistical potential, DFIRE, is shown to perform on par with the best current structure-based method in the literature, ProQres. A combination of different statistical potentials and structural features using support vector machines is shown to provide somewhat improved performance over published methods.
authors.affiliation: Howard Hughes Medical Institute at Columbia University, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, New York, New York 10032, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Fasnacht
authors.forename: Jiang
authors.initials: J
authors.lastname: Zhu
authors.forename: Barry
authors.initials: B
authors.lastname: Honig
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D019295:Computational Biology; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D011506:Proteins / Q000737:chemistry; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins