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An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design

Vizcarra, Christina L. and Zhang, Naigong and Marshall, Shannon A. and Wingreen, Ned S. and Zeng, Chen and Mayo, Stephen L. (2008) An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. Journal of Computational Chemistry, 29 (7). pp. 1153-1162. ISSN 0192-8651. http://resolver.caltech.edu/CaltechAUTHORS:20110617-165335622

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Abstract

Our goal is to develop accurate electrostatic models that can be implemented in current computational protein design protocols. To this end, we improve upon a previously reported pairwise decomposable, finite difference Poisson-Boltzmann (FDPB) model for protein design (Marshall et al., Protein Sci 2005, 14, 1293). The improvement involves placing generic sidechains at positions with unknown amino acid identity and explicitly capturing two-body perturbations to the dielectric environment. We compare the original and improved FDPB methods to standard FDPB calculations in which the dielectric environment is completely determined by protein atoms. The generic sidechain approach yields a two to threefold increase in accuracy per residue or residue pair over the original pairwise FDPB implementation, with no additional computational cost. Distance dependent dielectric and solvent-exclusion models were also compared with standard FDPB energies. The accuracy of the new pairwise FDPB method is shown to be superior to these models, even after reparameterization of the solvent-exclusion model.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1002/jcc.20878 DOIUNSPECIFIED
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20878/abstract;jsessionid=03BE8B4170F703D751F48810968C0A59.d03t01PublisherUNSPECIFIED
Contact Email Address:steve@mayo.caltech.edu
Additional Information:© 2007 Wiley Periodicals, Inc. Received 16 December 2006; Revised 1 October 2007; Accepted 17 October 2007. Article first published online: 11 Dec. 2007.
Subject Keywords:Static Electricity, Reproducibility of Results, Thermodynamics, Computational Biology, Computer Simulation, Computer-Aided Design, Models: Chemical, Amino Acids, Proteins, Poisson Distribution, Poisson-Boltzmann, Protein Design, Continuum Solvation, Electrostatics
Record Number:CaltechAUTHORS:20110617-165335622
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20110617-165335622
Official Citation:Vizcarra, C. L., Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C. and Mayo, S. L. (2008), An improved pairwise decomposable finite-difference Poisson–Boltzmann method for computational protein design. Journal of Computational Chemistry, 29: 1153–1162. doi: 10.1002/jcc.20878
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:24050
Collection:CaltechAUTHORS
Deposited By: Marie Ary
Deposited On:20 Jun 2011 23:16
Last Modified:04 Oct 2016 19:13

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