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

ABSTRACT: We have developed a method to predict ligand-binding 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).

SUBMITTER: Kinoshita K

PROVIDER: S-EPMC1933152 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

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eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

Kinoshita Kengo K Murakami Yoichi Y Nakamura Haruki H

Nucleic acids research 20070612 Web Server issue

We have developed a method to predict ligand-binding 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 ...[more]

PMID: 17567616

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Dataset Information

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

Publications

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

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