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image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Journal of Computati...arrow_drop_down
image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
Journal of Computational Chemistry
Article . 2003 . Peer-reviewed
License: Wiley Online Library User Agreement
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DBLP
Article . 2003
Data sources: DBLP
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Generalized born model with a simple smoothing function

Authors: Wonpil Im; Michael S. Lee; Charles L. Brooks III;

Generalized born model with a simple smoothing function

Abstract

AbstractBased on recent developments in generalized Born (GB) theory that employ rapid volume integration schemes (M. S. Lee, F. R. Salabury, Jr., and C. L. Brooks III, J Chem Phys 2002, 116, 10606) we have recast the calculation of the self‐electrostatic solvation energy to utilize a simple smoothing function at the dielectric boundary. The present GB model is formulated in this manner to provide consistency with the Poisson–Boltzmann (PB) theory previously developed to yield numerically stable electrostatic solvation forces based on finite‐difference methods (W. Im, D. Beglov, and B. Roux, Comp Phys Commun 1998, 111, 59). Our comparisons show that the present GB model is indeed an efficient and accurate approach to reproduce corresponding PB solvation energies and forces. With only two adjustable parameters—a0 to modulate the Coulomb field term, and a1 to include a correction term beyond Coulomb field—the PB solvation energies are reproduced within 1% error on average for a variety of proteins. Detailed analysis shows that the PB energy can be reproduced within 2% absolute error with a confidence of about 95%. In addition, the solvent‐exposed surface area of a biomolecule, as commonly used in calculations of the nonpolar solvation energy, can be calculated accurately and efficiently using the simple smoothing function and the volume integration method. Our implicit solvent GB calculations are about 4.5 times slower than the corresponding vacuum calculations. Using the simple smoothing function makes the present GB model roughly three times faster than GB models, which attempt to mimic the Lee–Richards molecular volume. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1691–1702, 2003

Related Organizations
Keywords

Macromolecular Substances, Protein Conformation, Static Electricity, Proteins, Hydrogen Bonding, Models, Theoretical, Energy Transfer, Solvents, Thermodynamics, Mathematical Computing

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
628
Top 1%
Top 1%
Top 1%
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