EF-seek: Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape

Kengo Kinoshita, Yoichi Murakami, Haruki Nakamura

Research output: Contribution to journalArticlepeer-review

49 Citations (Scopus)

Abstract

We have developed a method to predict ligandbinding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

Original languageEnglish
Pages (from-to)W398-W402
JournalNucleic acids research
Volume35
Issue numberSUPPL.2
DOIs
Publication statusPublished - 2007 Jul
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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