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eF-site and PDBjViewer: database and viewer for protein functional sites
Kengo Kinoshita1, Haruki Nakamura
1Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
Bioinformatics (Oxford, England)
|February 12, 2004
Summary
The electrostatic-surface of functional site (eF-site) database now features PDBjViewer for interactive 3D molecular surface and atomic model browsing. This tool enhances exploration of protein functional sites.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- The electrostatic-surface of functional site (eF-site) is a valuable resource for protein functional site molecular surfaces.
- Access to detailed molecular surface information is crucial for understanding protein function.
Purpose of the Study:
- To develop an interactive tool for visualizing molecular surfaces and atomic models within the eF-site database.
- To enhance the usability and accessibility of the eF-site database for researchers.
Main Methods:
- Development of a new three-dimensional interactive viewer, PDBjViewer.
- Implementation of PDBjViewer as both an applet and a stand-alone program.
Main Results:
- PDBjViewer enables seamless browsing of molecular surfaces alongside their corresponding atomic models.
- The viewer facilitates interactive exploration of protein functional sites.
Conclusions:
- The integration of PDBjViewer significantly improves the visualization capabilities of the eF-site database.
- This advancement provides researchers with a powerful tool for studying protein functional sites.