ArticleComputational & theoretical chemistry2013
Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.
Article in Computational & theoretical chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Benchmark of Available Explicit Solvent Models in CHARMM36m to Characterize Glycosaminoglycans.The journal of physical chemistry. B · 2025Article
- Testing a Heterogeneous Polarizable Continuum Model against Exact Poisson Boundary Conditions.Journal of chemical theory and computation · 2025Article
- Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the Second-Generation Mining Minima Method.Journal of chemical theory and computation · 2024Article
- Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations.Journal of chemical theory and computation · 2021Article
- Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations.Journal of chemical theory and computation · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- A size-modified poisson-boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage-dependent anion channel.Journal of computational chemistry · 2020Article
- Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 2019Article
- Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.Journal of chemical information and modeling · 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
- Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling.The journal of physical chemistry. B · 2017Article
- 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
- Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.Journal of computational chemistry · 2017Article
- DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.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
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Authors and funding
6 authors.
Funding
Abstract
Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. In this study, we have explored a second-order finite-difference numerical method to solve the widely used Poisson-Boltzmann equation for electrostatic analyses of realistic bio-molecules. The so-called immersed interface method was first validated and found to be consistent with the classical weighted harmonic averaging method for a diversified set of test biomolecules. The numerical accuracy and convergence behaviors of the new method were next analyzed in its computation of numerical reaction field grid potentials, energies, and atomic solvation forces. Overall similar convergence behaviors were observed as those by the classical method. Interestingly, the new method was found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface, though the numerical advantage of the new method is reduced when grid potentials are extrapolated to the molecular surface. Our exploratory study indicates the need for further improving interpolation/extrapolation schemes in addition to the developments of higher-order numerical methods that have attracted most attention in the field.
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