title: Identification of protein biochemical functions by similarity search using the molecular surface database eF-site.
abstract: The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrostatic surface of functional-site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide-binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.
authors.affiliation: Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan. kinoshita@tsurumi.yokohama-cu.ac.jp
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins