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FACTS: Fast analytical continuum treatment of solvation


Haberthür, U; Caflisch, A (2008). FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry, 29(5):701-715.

Abstract

An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume and spatial symmetry of the solvent that is displaced from around a solute atom by its neighboring atoms. The two measures of solvent displacement are combined in empirical equations to approximate the atomic (or self) electrostatic solvation energy and the solvent accessible surface area. The former directly yields the effective Born radius, which is used in the generalized Born (GB) formula to calculate the solvent-screened electrostatic interaction energy. A comparison with finite-difference Poisson data shows that atomic solvation energies, pair interaction energies, and their sums are evaluated with a precision comparable to the most accurate GB implementations. Furthermore, solvation energies of a large set of protein conformations have an error of only 1.5%. The solvent accessible surface area is used to approximate the nonpolar contribution to solvation. The empirical approach, called FACTS (Fast Analytical Continuum Treatment of Solvation), is only four times slower than using the vacuum energy in molecular dynamics simulations of proteins. Notably, the folded state of structured peptides and proteins is stable at room temperature in 100-ns molecular dynamics simulations using FACTS and the CHARMM force field.

Abstract

An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume and spatial symmetry of the solvent that is displaced from around a solute atom by its neighboring atoms. The two measures of solvent displacement are combined in empirical equations to approximate the atomic (or self) electrostatic solvation energy and the solvent accessible surface area. The former directly yields the effective Born radius, which is used in the generalized Born (GB) formula to calculate the solvent-screened electrostatic interaction energy. A comparison with finite-difference Poisson data shows that atomic solvation energies, pair interaction energies, and their sums are evaluated with a precision comparable to the most accurate GB implementations. Furthermore, solvation energies of a large set of protein conformations have an error of only 1.5%. The solvent accessible surface area is used to approximate the nonpolar contribution to solvation. The empirical approach, called FACTS (Fast Analytical Continuum Treatment of Solvation), is only four times slower than using the vacuum energy in molecular dynamics simulations of proteins. Notably, the folded state of structured peptides and proteins is stable at room temperature in 100-ns molecular dynamics simulations using FACTS and the CHARMM force field.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2008
Deposited On:09 Dec 2008 08:20
Last Modified:05 Apr 2016 12:38
Publisher:Wiley-Blackwell
ISSN:0192-8651
Publisher DOI:https://doi.org/10.1002/jcc.20832
PubMed ID:17918282

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