ASAView: database and tool for solvent accessibility representation in proteins - PubMed (original) (raw)
ASAView: database and tool for solvent accessibility representation in proteins
Shandar Ahmad et al. BMC Bioinformatics. 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.
Figures
Figure 1
ASAView of a DNA binding protein (PDB code 1CMA chain A). (a) The spiral view, which shows amino acid residues of 1CMA, in the order of their solvent accessibility. Most accessible residues come on the outermost ring of this spiral. Blue, red, green, gray colors are used for positively charged, negatively charged, polar and non-polar residues respectively. Yellow color is used for Cystein residues. Radius of the solid circles representing these residues corresponds to the relative solvent accessibility (b) Solvent accessibility of residues, with residues arranged in the original order as in their PDB file. Length of the bar represents the ASA in units relative to extended state ASA of that residue.
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References
- Rost B, Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins. 1994;20:216–226. - PubMed
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