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J Chem Theory Comput. 2013 Apr 9;9(4):2020-2034.

Improved Generalized Born Solvent Model Parameters for Protein Simulations.

Author information

1
Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 ; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794.
2
Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 ; Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112.

Abstract

The generalized Born (GB) model is one of the fastest implicit solvent models and it has become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with tradeoffs, and many reports in the literature have pointed out weaknesses with GB models. Because the quality of a GB model is heavily affected by empirical parameters used in calculating solvation energy, in this work we have refit these parameters for GB-Neck, a recently developed GB model, in order to improve the accuracy of both the solvation energy and effective radii calculations. The data sets used for fitting are significantly larger than those used in the past. Comparing to other pairwise GB models like GB-OBC and the original GB-Neck, the new GB model (GB-Neck2) has better agreement to Poisson-Boltzmann (PB) in terms of reproducing solvation energies for a variety of systems ranging from peptides to proteins. Secondary structure preferences are also in much better agreement with those obtained from explicit solvent MD simulations. We also obtain near-quantitative reproduction of experimental structure and thermal stability profiles for several model peptides with varying secondary structure motifs. Extension to non-protein systems will be explored in the future.

KEYWORDS:

GBSA; Generalized Born; Implicit solvent; perfect radii; protein folding; solvation energy

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