Current Computer-Aided Drug Design

Subhash C. Basak
Departments of Chemistry, Biochemistry & Molecular Biology University of Minnesota Duluth
Duluth, MN 55811
USA

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Role of Solvent Accessibility in Structure Based Drug Design

Author(s): M. Michael Gromiha, Shandar Ahmad.

Abstract:

Solvent accessibility plays an important role to the structure and function of biological macromolecules. Generally amino acid residues located in the surface of a protein serve as active sites and/or interact with other molecules and ligands. In this review, we briefly define the concept of solvent accessibility with computational procedure. The methods available for calculating solvent accessibility of molecules from their three-dimensional structures and predicting the accessibility from amino acid sequences have been described. The salient features of the solvent accessibility of amino acid residues/nucleotides/sugars in biomolecular structures and its importance for the stability of biomacromolecules have been explored. Further, the application of solvent accessibility for identifying active site residues, binding sites in DNA binding proteins and functionally important residues in membrane proteins will be discussed. The information about the accessible surface area of the basic units of biomacromolecules will be very helpful for de novo protein and drug design.

Keywords: solvent accessibility, drug design, active site, structure, prediction

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Article Details

VOLUME: 1
ISSUE: 3
Year: 2005
Page: [223 - 235]
Pages: 13
DOI: 10.2174/1573409054367664
Price: $58