A linear function for the approximation of accessible surface area of proteins.
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.
Kim
Ryang Guk
RG
Interdisciplinary Program for Biochemical Engineering and Biotechnology, College of Engineering, Seoul National University, Seoul, 151-744, Korea.
Choi
Cha-Yong
CY
D000465:Algorithms; D008956:Models, Chemical; D008958:Models, Molecular; D019151:Peptide Library; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties
D019151:Peptide Library; D011506:Proteins