Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes

2015 ◽  
Vol 36 (9) ◽  
pp. 585-596 ◽  
Author(s):  
Federico Fogolari ◽  
Alessandra Corazza ◽  
Gennaro Esposito
Keyword(s):  
Boltzmann Equation ◽  
Nucleic Acid ◽  
Protein Complexes ◽  
Accuracy Assessment ◽  
Generalized Born ◽  
Born Model ◽  
Acid Protein ◽  
Generalized Born Model ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

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.

Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK

Biopolymers ◽  
2004 ◽  
Vol 73 (2) ◽  
pp. 192-204 ◽  
Author(s):  
Xinshan Kang ◽  
Richard H. Shafer ◽  
Irwin D. Kuntz
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Binding ◽  
Free Energies ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model ◽  
Binding Free Energies

scholarly journals Monte Carlo methods for linear and non-linear Poisson-Boltzmann equation

2015 ◽  
Vol 48 ◽  
pp. 420-446 ◽  
Author(s):  
Mireille Bossy ◽  
Nicolas Champagnat ◽  
Hélène Leman ◽  
Sylvain Maire ◽  
Laurent Violeau ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Boltzmann Equation ◽  
Monte Carlo Methods ◽  
Non Linear ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

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
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