title: Predicting enzymatic function from global binding site descriptors.
abstract: Due to the rising number of solved protein structures, computer-based techniques for automatic protein functional annotation and classification into families are of high scientific interest. DoGSiteScorer automatically calculates global descriptors for self-predicted pockets based on the 3D structure of a protein. Protein function predictors on three levels with increasing granularity are built by use of a support vector machine (SVM), based on descriptors of 26632 pockets from enzymes with known structure and enzyme classification. The SVM models represent a generalization of the available descriptor space for each enzyme class, subclass, and substrate-specific sub-subclass. Cross-validation studies show accuracies of 68.2% for predicting the correct main class and accuracies between 62.8% and 80.9% for the six subclasses. Substrate-specific recall rates for a kinase subset are 53.8%. Furthermore, application studies show the ability of the method for predicting the function of unknown proteins and gaining valuable information for the function prediction field.
authors.affiliation: University of Hamburg, Center for Bioinformatics, Bundesstr 43, 20146 Hamburg, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Volkamer
authors.forename: Daniel
authors.initials: D
authors.lastname: Kuhn
authors.forename: Friedrich
authors.initials: F
authors.lastname: Rippmann
authors.forename: Matthias
authors.initials: M
authors.lastname: Rarey
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000737:chemistry / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D004789:Enzyme Activation; D008024:Ligands; D058977:Molecular Sequence Annotation; D010770:Phosphotransferases / Q000737:chemistry* / Q000145:classification; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D060388:Support Vector Machine
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D010770:Phosphotransferases