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A new analytical method for computing solvent‐accessible surface area of macromolecules and its gradients
Author(s) -
Hayryan Shura,
Hu ChinKun,
Skřivánek Jaroslav,
Hayryane Edik,
Pokorný Imrich
Publication year - 2005
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20125
Subject(s) - intersection (aeronautics) , surface (topology) , plane (geometry) , macromolecule , transformation (genetics) , computer science , space (punctuation) , algorithm , computational science , mathematics , geometry , chemistry , biochemistry , engineering , gene , aerospace engineering , operating system
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. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 334–343, 2005