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Literature DB >> 23745011

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

Abstract

We review recent developments of fast analytical methods for macroscopic electrostatic calculations in biological applications, including the Poisson-Boltzmann (PB) and the generalized Born models for electrostatic solvation energy. The focus is on analytical approaches for hybrid solvation models, especially the image charge method for a spherical cavity, and also the generalized Born theory as an approximation to the PB model. This review places much emphasis on the mathematical details behind these methods.

Entities: Chemical Disease Gene

Keywords: Poisson–Boltzmann equation; electrostatic free energy; electrostatic interactions; fast algorithm; generalized Born theory; hybrid explicit/implicit solvation models; image charge approximation; macroscopic solvent models; multipole expansion; reaction field

Year: 2011 PMID： 23745011 PMCID： PMC3671632 DOI： 10.1137/090774288

Source DB: PubMed Journal: SIAM Rev Soc Ind Appl Math ISSN： 0036-1445 Impact factor: 10.780

95 in total

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Authors:
Journal: J Colloid Interface Sci Date: 1999-05-01 Impact factor: 8.128

2. Effective Born radii in the generalized Born approximation: the importance of being perfect.

Authors: Alexey Onufriev; David A Case; Donald Bashford
Journal: J Comput Chem Date: 2002-11-15 Impact factor: 3.376

3. Implicit solvation based on generalized Born theory in different dielectric environments.

Authors: Michael Feig; Wonpil Im; Charles L Brooks
Journal: J Chem Phys Date: 2004-01-08 Impact factor: 3.488

4. An efficient hybrid explicit/implicit solvent method for biomolecular simulations.

Authors: Michael S Lee; Freddie R Salsbury; Mark A Olson
Journal: J Comput Chem Date: 2004-12 Impact factor: 3.376

5. Free Energy Calculations for DNA Near Surfaces Using an Ellipsoidal Geometry.

Authors: J Ambia-Garrido; B Montgomery Pettitt
Journal: Commun Comput Phys Date: 2008-01-01 Impact factor: 3.246

6. Computation of molecular electrostatics with boundary element methods.

Authors: J Liang; S Subramaniam
Journal: Biophys J Date: 1997-10 Impact factor: 4.033

7. A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins.

Authors: Eng-Hui Yap; Teresa Head-Gordon
Journal: J Chem Theory Comput Date: 2010-06-17 Impact factor: 6.006

8. Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models.

Authors: Abhishek K Jha; Karl F Freed
Journal: J Chem Phys Date: 2008-01-21 Impact factor: 3.488

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

1. Long-Range Electrostatic Attractions between Identically Charged Particles in Confined Geometries: An Unresolved Problem.

2. Effective Born radii in the generalized Born approximation: the importance of being perfect.

3. Implicit solvation based on generalized Born theory in different dielectric environments.

4. An efficient hybrid explicit/implicit solvent method for biomolecular simulations.

5. Free Energy Calculations for DNA Near Surfaces Using an Ellipsoidal Geometry.

6. Computation of molecular electrostatics with boundary element methods.

7. A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins.

8. Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models.

9. Generalized born model with a simple smoothing function.

10. Highly accurate biomolecular electrostatics in continuum dielectric environments.

Review 1. Generalized Born Implicit Solvent Models for Biomolecules.

2. Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding.

3. Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model.