Article
Rank-ordering protein-ligand binding affinity by a quantum mechanics/ molecular mechanics/Poisson-Boltzmann-surface area model
Journal of Chemical Physics
(2007)
Abstract
The authors describe a quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area model for rank-ordering protein-ligand binding affinity in aqueous solution. Unlike many classical continuum electrostatics calculations in which the protein and ligand are treated as a uniform dielectric, this model uses quantum mechanics to explicitly describe the electronic polarization of the ligand by its environment. In solving the Poisson-Boltzmann equation, the authors use the quantum mechanical charge density directly rather than the common point-charge approximation. The authors show that useful results can be obtained by using experimental structure, by choosing a protein dielectric constant that is smaller than that typically used in classical electrostatics calculations, and by performing the calculations in a manner that can improve the odds of cancellation of errors.
Disciplines
Publication Date
January 14, 2007
DOI
10.1063/1.2423029
Publisher Statement
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in [Wang, M., and Wong, C.F. (2007). Rank-ordering protein-ligand binding affinity by a quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area model. The Journal of Chemical Physics 126, 026101.] and may be found at https://doi.org/10.1063/1.2423029.
Citation Information
Mingliang Wang and Chung F. Wong. "Rank-ordering protein-ligand binding affinity by a quantum mechanics/ molecular mechanics/Poisson-Boltzmann-surface area model" Journal of Chemical Physics Vol. 126 Iss. 2 (2007) p. 26101 Available at: http://works.bepress.com/chung-wong/28/