eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
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).
Kinoshita
Kengo
K
Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan. kino@ims.u-tokyo.ac.jp
Murakami
Yoichi
Y
Nakamura
Haruki
H
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D030562:Databases, Protein; D021621:Imaging, Three-Dimensional / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D012984:Software; D055672:Static Electricity; D014584:User-Computer Interface
D008024:Ligands; D011506:Proteins