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

Kengo Kinoshita, Haruki Nakamura

Research output: Contribution to journalArticlepeer-review

77 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)711-718
Number of pages8
JournalProtein Science
Issue number3
Publication statusPublished - 2005 Mar


  • Hypothetical proteins
  • Protein three dimensional structure
  • Structural genomics
  • Structure-based function prediction


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