Poisson-Boltzmann methods

Nathan A. Baker, Biomolecular Applications of Poisson-Boltzmann Methods. 

These workers also calculated the relative stability of the tautomers lOa-c in the gas phase by ab initio and density functional theory (DFT) methods and in solution using several continuum solvation models such as self-consistent reaction fields (SCRF) and the Poisson-Boltzmann method. These results showed good agreement between the experimental and theoretical approaches. 

Baker, N. A. (2004). Poisson-Boltzmann methods for biomolecular electrostatics. Numer. Comput. Methods 383(Pt D), 94—118. 

Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002) Rapid grid-based construction of the molecular surface for both molecules and geometric objects applications to the finite difference Poisson-Boltzmann method, J Comp Chem, 23 128-137... 

K. Sharp,/. Comput. Chem., 12, 454 (1991). Incorporating Solvent and Ion Screening into Molecular Dynamics Using the Finite-Difference Poisson-Boltzmann Method. 

Numerical strategies for computing both the electronic and nuclear components of the ET rate are now rather advanced (see the chapter by Newton). For example, in both proteins and small molecules, finite-difference Poisson-Boltzmann methods are widely used for computing the outer-sphere component of the solvent reorganization energy Aq [9, 10, 11, 12] ... 

Vizcarra CL, Zhang NG, Marshall SA, Wingreen NS, Zeng C, Mayo SL (2008) An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. J Comput Chem 29 1153-1162... 

Prabhu, N.V., Zhu, P., Sharp, K.A. Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. J. Comput. Chem. 2004,25(16), 2049-64, December. 

Baker, N.A. (2005) Biomolecular applications of Poisson-Boltzmann methods, in Reviews in Computational Chemistry, vol. 21 (eds K.B. Lipkowitz, R. Larter, and T.R. Cundari), John Wiley Sons Inc., pp. 349-379. 

Poisson-Boltzmann methods offer a compromise between faster, but more approximate models such as GB, and more detailed explicit solvent and integral equation techniques. The remainder of this chapter is devoted to discussion of the implementation and application of PB and related methods. 

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