On methods for determining solvent accessible surface area for proteins in their unfolded state

BACKGROUND: There are many different methods for estimating solvent accessible surface area for proteins in their unfolded states. In this article, we compare eight methods, assessing whether or not they lead to different estimates of total accessible surface area as well as their impact on relationships with thermodynamic variables. FINDINGS: Our results demonstrate that most pairs of compared methods do result in different unfolded estimates of accessible surface area (only four pairs of methods do not yield significantly different estimates). However, we do not see a significant impact on the relationship between accessible surface area and thermodynamic parameters across the different methods. CONCLUSIONS: We advocate the use of the Gong and Rose transition midpoint method for computing solvent accessible surface area due to its computational ease, physical basis, and performance in terms of relationships with thermodynamic parameters.