Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies

2018 ◽  
Vol 123 (5) ◽  
pp. 957-973 ◽  
Author(s):  
Yoshio Okiyama ◽  
Chiduru Watanabe ◽  
Kaori Fukuzawa ◽  
Yuji Mochizuki ◽  
Tatsuya Nakano ◽  
...  
Keyword(s):  
Boltzmann Equation ◽  
Ligand Binding ◽  
Molecular Orbital ◽  
Implicit Solvent ◽  
Molecular Orbital Calculations ◽  
Binding System ◽  
Fragment Molecular Orbital ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study

2018 ◽  
Vol 122 (16) ◽  
pp. 4457-4471 ◽  
Author(s):  
Yoshio Okiyama ◽  
Tatsuya Nakano ◽  
Chiduru Watanabe ◽  
Kaori Fukuzawa ◽  
Yuji Mochizuki ◽  
...  
Keyword(s):  
Boltzmann Equation ◽  
Molecular Orbital ◽  
Implicit Solvent ◽  
Molecular Orbital Calculations ◽  
Fragment Molecular Orbital ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

scholarly journals A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications

2014 ◽  
Vol 2 (1) ◽  
pp. 86-97 ◽  
Author(s):  
Dexuan Xie ◽  
Yi Jiang ◽  
Jinyong Ying
Keyword(s):  
Finite Element ◽  
Boltzmann Equation ◽  
Continuum Model ◽  
Numerical Algorithms ◽  
Implicit Solvent ◽  
Numerical Comparison ◽  
Test Model ◽  
Comparison Study ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Abstract The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.

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
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