Derivatives of Molecular Surface Area and Volume: Simple and Exact Analytical Formulas

被引：30
|
作者：
Klenin, Konstantin V. [1 ,2 ]
Tristram, Frank [3 ]
Strunk, Timo [3 ]
Wenzel, Wolfgang [1 ,3 ]
机构：
[1] Karlsruhe Inst Technol, Ctr Funct Nanostruct, D-76049 Karlsruhe, Germany
[2] Karlsruhe Inst Technol, Steinbuch Ctr Comp, D-76021 Karlsruhe, Germany
[3] Karlsruhe Inst Technol, Inst Nanotechnol, D-76021 Karlsruhe, Germany
来源：
JOURNAL OF COMPUTATIONAL CHEMISTRY | 2011年 / 32卷 / 12期
关键词：
molecular modeling; implicit solvent models; solvent accessible surface area; molecular volume; power diagram; EXCLUDED-VOLUME; DYNAMICS SIMULATIONS; OVERLAPPING SPHERES; SOLUTE MOLECULES; FREE-ENERGIES; SOLVENT; SOLVATION; EFFICIENT; HYDRATION; MODEL;
D O I：
10.1002/jcc.21844
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2647-2653, 2011
引用
收藏
页码：2647 / 2653
页数：7
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