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5 (page number not for citation purposes) BMC Bioinformatics Open Access Database ASAView: Database and tool for solvent accessibility representation in proteins Shandar Ahmad*1, Michael Gromiha2, Hamed Fawareh3 and Akinori Sarai1 Address: 1Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka

820 8502, Fukuoka-ken, Japan, 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto- ku, Tokyo, Japan and 3Computer Science Department, Zarka Private University, Zarka 13110, Jordan Email: Shandar Ahmad* - shandar@bse.

kyutech.ac.jp;

Michael Gromiha - [email protected];

Hamed Fawareh - [email protected];

Akinori Sarai - [email protected] * Corresponding author 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. Background Key functional properties of proteins and so-called active amino acid sites strongly correlate with amino acid sol- vent accessibility or accessible surface area (ASA) [1,2]. For example, DNA-binding probability of a residue is sig- nificantly higher for residues with higher solvent accessi- ble area [2]. Recognizing the importance of ASA, several groups have developed methods for predicting it from amino acid sequence [3-7] similar to secondary structure prediction. We have recently developed a prediction server, which provides real-valued predictions of solvent accessibility rather than burial categories [8]. Although useful methods for representing secondary structures have been developed and are widely used, good tools for representing solvent accessibility have been con- spicuously missing. As a case in point PDBsum carries plots of secondary structure [9] but gives no mention of accessibility, which may be even more important for the estimate of active sites [10]. We have therefore developed a method to provide quick visualization of solvent acces- sibility in terms of a compact spiral plot, which may reveal deep insights into protein structure along with secondary structure, composition and other summary information. We also developed a tool to generate postscript graphical Published:

01 May

2004 BMC Bioinformatics 2004, 5:51 Received:

20 November

2003 Accepted:

01 May

2004 This article is available from: http://www.biomedcentral.com/1471-2105/5/51 ?

2004 Ahmad et al;

licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article'