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J Mol Graph Model. 1997 Dec;15(6):355-8, 386-8.

Graphical visualization of mean hydration from molecular dynamics simulations.

Author information

1
Graduate Group in Biophysics, University of California, San Francisco 94143, USA.

Abstract

How does one characterize water solvating a complex solute? Specific hydration of proteins and nucleic acids plays a key role in many biological processes. However, traditional pairwise descriptions of solvent structure (radial distribution functions, etc.) are incapable of adequately describing the hydration of these complex solutes. We have developed methods to visualize the average three-dimensional water structure surrounding a solute, as seen in a molecular dynamics (MD) simulation. Applications to simple solutes [sodium ion, N-methyl acetamide, 18-crown-6, (hydroxymethyl)phenols] are presented, and the extension of the method to larger molecules of biochemical interest is discussed.

PMID:
9704297
DOI:
10.1016/s1093-3263(98)00006-0
[Indexed for MEDLINE]

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