eF-site Help

From eF-site
(Redirected from EF-site Help)
Jump to: navigation, search

about eF-site

eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms. The Connolly surfaces were made by using the MSP program (Connolly, M.L., J. Mol.Graph., 4, 93-96, 1986) and the electrostatic potentials were calculated by solving Poisson-Boltzmann equations with the self-consistent boundary method by Nakamura, H. & Nishida, S. (J. Phys. Soc. Jpn., 56, 1609-1622, 1987).

seqinfo and efvet files

In this database system, two kinds of file, seqinfo file and efvet file, are used to keep all information for each entry. The seqinfo file describes biological functions of the molecule and chemical properties of each functional site on the molecular surface. The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are discribed together by the surface color in such a way that red to blue colors correspond negative to positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residue. The seqinfo file and efvet file are both written in XML and schema documents for them are available (seqinfo, efvet).

In eF-site Tools page, we provide a program that downloads efvet files as space separated values format. The format is based on that of the vet file of the MSP program described here with vertex lines being extended. The original vertex line has three placeholder columns for external programs, and the efvet file puts five values (electrostatic potential, hydrophobicity, temperature factor, minimum curvature and maximum curvature) there. Each vertex line has also atom data (extracted from the corresponding PDB ATOM record) at the end.


jV is used to display molecules and their surfaces as a Java applet program. The program 'jV' has been developed by Kengo Kinoshita (Graduate School of Information Sciences, Tohoku University) and Haruki Nakamura (Institute for Protein Research, Osaka Univeristy), as one of the activities of Protein Data Bank Japan (PDBj), supported by grant-in-aid from National Bioscience Database Center, Japan Science and Technology Agancy (JST-NBDC) and Institute for Protein Research IPR, Osaka University.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows.

Action Window, Linux Mac OS X
rotate around X,Y axes left drag drag
rotate around Z axis Shift + right drag Shift + command + drag
translate along X,Y axes right drag command + drag
translate along Z axis (zoom in/out) Shift + left drag Shift + drag

In order to use jV, the Java Runtime Environment (JRE) 1.6 or later must be installed on your computer. jV is freely distributed and can be used as a stand-alone program as well as an applet. In addition to mouse controls, a command line interface is provided.

Download jV