Identification of protein functions from a molecular surface database, eF-site

Kengo Kinoshita, Jun'ichi Furui, Haruki Nakamura

Research output: Contribution to journalArticlepeer-review

105 Citations (Scopus)

Abstract

A bioinformatics method was developed to identify the protein surface around the functional site and to estimate the biochemical function, using a newly constructed molecular surface database named the eF-site (electrostatic surface of Functional site. Molecular surfaces of protein molecules were computed based on the atom coordinates, and the eF-site database was prepared by adding the physical properties on the constructed molecular surfaces. The electrostatic potential on each molecular surface was individually calculated solving the Poisson-Boltzmann equation numerically for the precise continuum model, and the hydrophobicity information of each residue was also included. The eF-site database is accessed by the internet (http://pi.protein.osaka-u.ac.jp/eF-site/). We have prepared four different databases, eF-site/antibody, eF-site/prosite, eF-site/P-site, and eF-site/ActiveSite, corresponding to the antigen binding sites of antibodies with the same orientations, the molecular surfaces for the individual motifs in PROSITE database, the phosphate binding sites, and the active site surfaces for the representatives of the individual protein family, respectively. An algorithm using the clique detection method as an applied graph theory was developed to search of the eF-site database, so as to recognize and discriminate the characteristic molecular surfaces of the proteins. The method identifies the active site having the similar function to those of the known proteins.

Original languageEnglish
Pages (from-to)9-22
Number of pages14
JournalJournal of Structural and Functional Genomics
Volume2
Issue number1
DOIs
Publication statusPublished - 2002
Externally publishedYes

Keywords

  • Active site
  • Antibody
  • Electrostatic potential
  • Molecular surface
  • Structure database
  • Structure-based function prediction

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Genetics

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