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Identification of the ligand binding sites on the molecular surface of proteins

¹ Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
² PRESTO, JST, Kawaguchi, Saitama 332-0012, Japan

(RECEIVED August 29, 2004; FINAL REVISION November 9, 2004; ACCEPTED November 10, 2004)

Identification of protein biochemical functions based on their three-dimensional structures is now required in the post–genome-sequencing era. Ligand binding is one of the major biochemical functions of proteins, and thus the identification of ligands and their binding sites is the starting point for the function identification. Previously we reported our first trial on structure-based function prediction, based on the similarity searches of molecular surfaces against the functional site database. Here we describe the extension of our first trial by expanding the search database to whole heteroatom binding sites appearing within the Protein Data Bank (PDB) with the new analysis protocol. In addition, we have determined the similarity threshold line, by using 10 structure pairs with solved free and complex structures. Finally, we extensively applied our method to newly determined hypothetical proteins, including some without annotations, and evaluated the performance of our methods.

Keywords: structure-based function prediction; hypothetical proteins; structural genomics; protein three dimensional structure

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041080105.

Reprint requests to: Kengo Kinoshita, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; e-mail: kino{at}ims.u-tokyo.ac.jp; fax: 81-3-5449-5133.

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