eF-site

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).

molmil

See the main article on molmil for more information.

jV

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 applets are displayed. The structure of the molecule is shown in the left applet and the molecular surface is displayed in the right applet. The mouse controls are 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

• binary (4.4.3)
• source code (4.4.3) (registration will be required)