scholarly journals Electrostatics of Ligand Binding:  Parametrization of the Generalized Born Model and Comparison with the Poisson−Boltzmann Approach

2006 ◽  
Vol 110 (18) ◽  
pp. 9304-9313 ◽  
Author(s):  
Hao-Yang Liu ◽  
Xiaoqin Zou
Keyword(s):  
Ligand Binding ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model ◽  
Poisson Boltzmann

scholarly journals A Stochastic Solver of the Generalized Born Model

2013 ◽  
Vol 1 ◽  
pp. 63-74 ◽  
Author(s):  
Robert C. Harris ◽  
Travis Mackoy ◽  
Marcia O. Fenley
Keyword(s):  
Protein Complexes ◽  
Binding Energies ◽  
Generalized Born ◽  
Born Model ◽  
Solvation Energies ◽  
Generalized Born Model ◽  
Poisson Boltzmann ◽  
Peptide Complexes ◽  
Poisson Boltzmann Equation ◽  
Better Than

AbstractA stochastic generalized Born (GB) solver is presented which can give predictions of energies arbitrarily close to those that would be given by exact effective GB radii, and, unlike analytical GB solvers, these errors are Gaussian with estimates that can be easily obtained from the algorithm. This method was tested by computing the electrostatic solvation energies (ΔGsolv) and the electrostatic binding energies (ΔGbind) of a set of DNA-drug complexes, a set of protein-drug complexes, a set of protein-protein complexes, and a set of RNA-peptide complexes. Its predictions of ΔGsolv agree with those of the linearized Poisson-Boltzmann equation, but it does not predict ΔGbind well, although these predictions of ΔGbind may be marginally better than those of traditional analytical GB solvers. Apparently, the GB model itself must be improved before accurate estimates of ΔGbind can be obtained.

Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field

2004 ◽  
Vol 108 (41) ◽  
pp. 16264-16270 ◽  
Author(s):  
William L. Jorgensen ◽  
Jakob P. Ulmschneider ◽  
Julian Tirado-Rives
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model

scholarly journals Modification of the Generalized Born Model Suitable for Macromolecules

2000 ◽  
Vol 104 (15) ◽  
pp. 3712-3720 ◽  
Author(s):  
Alexey Onufriev ◽  
Donald Bashford ◽  
David A. Case
Keyword(s):  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model
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