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Open Access Database

ASAView: Database and tool for solvent accessibility representation in proteins

Shandar Ahmad1*, Michael Gromiha2, Hamed Fawareh3 and Akinori Sarai1

Author Affiliations

1 Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka-ken, Japan

2 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, Japan

3 Computer Science Department, Zarka Private University, Zarka 13110, Jordan

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BMC Bioinformatics 2004, 5:51  doi:10.1186/1471-2105-5-51

Published: 1 May 2004

Abstract

Background

Accessible surface area (ASA) or solvent accessibility of amino acids in a protein has important implications. Knowledge of surface residues helps in locating potential candidates of active sites. Therefore, a method to quickly see the surface residues in a two dimensional model would help to immediately understand the population of amino acid residues on the surface and in the inner core of the proteins.

Results

ASAView is an algorithm, an application and a database of schematic representations of solvent accessibility of amino acid residues within proteins. A characteristic two-dimensional spiral plot of solvent accessibility provides a convenient graphical view of residues in terms of their exposed surface areas. In addition, sequential plots in the form of bar charts are also provided. Online plots of the proteins included in the entire Protein Data Bank (PDB), are provided for the entire protein as well as their chains separately.

Conclusions

These graphical plots of solvent accessibility are likely to provide a quick view of the overall topological distribution of residues in proteins. Chain-wise computation of solvent accessibility is also provided.