title: A hybrid method for protein-protein interface prediction.
abstract: The growing structural coverage of proteomes is making structural comparison a powerful tool for function annotation. Such template-based approaches are based on the observation that structural similarity is often sufficient to infer similar function. However, it seems clear that, in addition to structural similarity, the specific characteristics of a given protein should also be taken into account in predicting function. Here we describe PredUs 2.0, a method to predict regions on a protein surface likely to bind other proteins, that is, interfacial residues. PredUs 2.0 is based on the PredUs method that is entirely template-based and uses known binding sites in structurally similar proteins to predict interfacial residues. PredUs 2.0 uses a Bayesian approach to combine the template-based scoring of PredUs with a score that reflects the propensities of individual amino acids to be in interfaces. PredUs 2.0 includes a novel protein size dependent metric to determine the number of residues that should be reported as interfacial. PredUs 2.0 significantly outperforms PredUs as well as other published interface prediction methods.
authors.affiliation: Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St. Nicholas Ave., Room 815, New York, NY, 10032.
authors.forename: Howook
authors.initials: H
authors.lastname: Hwang
authors.affiliation: Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St. Nicholas Ave., Room 815, New York, NY, 10032.
authors.forename: Donald
authors.initials: D
authors.lastname: Petrey
authors.affiliation: Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St. Nicholas Ave., Room 815, New York, NY, 10032.
authors.forename: Barry
authors.initials: B
authors.lastname: Honig
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: Bayesian network; interface prediction; interface propensity; protein surface patch; structural similarity; template