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Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site
Author(s) -
Kinoshita Kengo,
Nakamura Haruki
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0368703
Subject(s) - methanococcus , structural similarity , protein data bank , computational biology , similarity (geometry) , structural genomics , surface protein , binding site , chemistry , identification (biology) , biology , protein structure , database , biochemistry , gene , computer science , artificial intelligence , image (mathematics) , botany , escherichia coli , virology
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.