Generalized Born Models of Macromolecular Solvation Effects

Annual Review of Physical Chemistry - Tập 51 Số 1 - Trang 129-152 - 2000
Donald Bashford1, David A. Case2
1Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA. [email protected]
2Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037

Tóm tắt

▪ Abstract  It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

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Annual Review of Physical Chemistry

Tập 51 Số 1

129-152

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