title: A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients.
abstract: In the calculation of thermodynamic properties and three-dimensional structures of macromolecules, such as proteins, it is important to have an efficient algorithm for computing the solvent-accessible surface area of macromolecules. Here, we propose a new analytical method for this purpose. In the proposed algorithm we consider the transformation that maps the spherical circles formed by intersection of the atomic surfaces in three-dimensional space onto the circles on a two-dimensional plane, and the problem of computing the solvent-accessible surface area is reduced to the problem of computing the corresponding curve integrals on the plane. This allows to consider only the integrals along the circular trajectories on the plane. The algorithm is suitable for parallelization. Testings on many proteins as well as the comparison to the other analogous algorithms have shown that our method is accurate and efficient.
authors.affiliation: Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China.
authors.forename: Shura
authors.initials: S
authors.lastname: Hayryan
authors.forename: Chin-Kun
authors.initials: CK
authors.lastname: Hu
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Skrivánek
authors.forename: Edik
authors.initials: E
authors.lastname: Hayryane
authors.forename: Imrich
authors.initials: I
authors.lastname: Pokorný
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D046911:Macromolecular Substances; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D046911:Macromolecular Substances; D011506:Proteins