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Literature DB >> 15837170

Improving implicit solvent simulations: a Poisson-centric view.

Abstract

Recent developments in implicit solvent models may be compared in terms of accuracy and computational efficiency. Based on improvements in the accuracy of generalized Born methods and the speed of Poisson-Boltzmann solvers, it appears that the two techniques are converging to a point at which both will be suitable for simulating certain types of biomolecular systems over sizable time and length scales.

Mesh：

Substances：
Biopolymers
Solvents

Year: 2005 PMID： 15837170 DOI： 10.1016/j.sbi.2005.02.001

Source DB: PubMed Journal: Curr Opin Struct Biol ISSN： 0959-440X Impact factor: 6.809

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Cited

135 in total

1. Differential geometry based solvation model II: Lagrangian formulation.

Authors: Zhan Chen; Nathan A Baker; G W Wei
Journal: J Math Biol Date: 2011-01-30 Impact factor: 2.259

2. Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state.

Authors: Nariman Naber; Adam Larson; Sarah Rice; Roger Cooke; Edward Pate
Journal: J Mol Biol Date: 2011-01-26 Impact factor: 5.469

3. Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

Authors: Enrico O Purisima; Christopher R Corbeil; Traian Sulea
Journal: J Comput Aided Mol Des Date: 2010-04-06 Impact factor: 3.686

4. A comparable study of image approximations to the reaction field.

Authors: Shaozhong Deng; Wei Cai; Donald Jacobs
Journal: Comput Phys Commun Date: 2007-11-01 Impact factor: 4.390

5. An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Authors: Yuchun Lin; Andrij Baumketner; Shaozhong Deng; Zhenli Xu; Donald Jacobs; Wei Cai
Journal: J Chem Phys Date: 2009-10-21 Impact factor: 3.488

Improving implicit solvent simulations: a Poisson-centric view.

1. Differential geometry based solvation model II: Lagrangian formulation.

2. Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state.

3. Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

4. A comparable study of image approximations to the reaction field.

5. An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

6. Generalized Born model with a simple, robust molecular volume correction.

7. New Versions of Image Approximations to the Ionic Solvent Induced Reaction Field.

8. Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.

9. Packing interface energetics in different crystal forms of the λ Cro dimer.

10. LS-VISM: A software package for analysis of biomolecular solvation.