A Linear Function for the Approximation of Accessible Surface Area of Proteins

Title: A Linear Function for the Approximation of Accessible Surface Area of Proteins

Volume: 13 Issue: 6

Author(s): Ryang G. Kim and Cha-Yong Choi

Affiliation:

Keywords: Accessible surface area, linear function, linear regression, unified atom

Abstract: Since the solvent accessible surface area of proteins has been utilized as an important factor in the prediction of their thermodynamic properties, a simple and analytical method for its determination would contribute to protein structure prediction and analysis methods. We report the development of a simple and analytical method for the estimation of the accessible surface area of protein, consisting of linear functions of distances between unified atoms. While our formulation was much simpler than previously developed methods, it showed comparable performance, with the mean relative error on total solvent accessible surface area of 0.49 and 2.16% for 89 denatured and native protein structures, respectively. Moreover, the partial derivatives of accessible surface area to the position of unified atoms could also be derived in a simpler form.

Cite this article as:

Kim G. Ryang and Choi Cha-Yong, A Linear Function for the Approximation of Accessible Surface Area of Proteins, Protein & Peptide Letters 2006; 13 (6) . https://dx.doi.org/10.2174/092986606777145869

DOI https://dx.doi.org/10.2174/092986606777145869	Print ISSN 0929-8665
Publisher Name Bentham Science Publisher	Online ISSN 1875-5305