ArticlePhysical chemistry chemical physics : PCCP2013
Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications.
Article in Physical chemistry chemical physics : PCCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 2019Article
- An efficient second-order poisson-boltzmann method.Journal of computational chemistry · 2019Article
- Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.Journal of chemical information and modeling · 2019Article
- Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.The Journal of chemical physics · 2017Article
- A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.Journal of chemical theory and computation · 2017Article
- Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.Journal of chemical theory and computation · 2017Article
- Numerical interpretation of molecular surface field in dielectric modeling of solvation.Journal of computational chemistry · 2017Article
- Recent Developments and Applications of the MMPBSA Method.Frontiers in molecular biosciences · 2017Review
- Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor.The journal of physical chemistry. B · 2016Article
- Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis.Journal of computational chemistry · 2016Article
- Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions.The journal of physical chemistry. B · 2016Article
- Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.Journal of computational chemistry · 2014Article
- Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.Computational & theoretical chemistry · 2013Article
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6 authors.
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Abstract
Continuum solvent treatments based on the Poisson-Boltzmann equation have been widely accepted for energetic analysis of biomolecular systems. In these approaches, the molecular solute is treated as a low dielectric region and the solvent is treated as a high dielectric continuum. The existence of a sharp dielectric jump at the solute-solvent interface poses a challenge to model the solvation energetics accurately with such a simple mathematical model. In this study, we explored and evaluated a strategy based on the "induced surface charge" to eliminate the dielectric jump within the finite-difference discretization scheme. In addition to the use of the induced surface charges in solving the equation, the second-order accurate immersed interface method is also incorporated to discretize the equation. The resultant linear system is solved with the GMRES algorithm to explicitly impose the flux conservation condition across the solvent-solute interface. The new strategy was evaluated on both analytical and realistic biomolecular systems. The numerical tests demonstrate the feasibility of utilizing induced surface charge in the finite-difference solution of the Poisson-Boltzmann equation. The analysis data further show that the strategy is consistent with theory and the classical finite-difference method on the tested systems. Limitations of the current implementations and further improvements are also analyzed and discussed to fully bring out its potential of achieving higher numerical accuracy.
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