ArticleSIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics2011
AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS.
Article in SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics, 2011. 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.
- Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES.Journal of computational chemistry · 2024Article
- Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation.Journal of computational physics · 2020Article
- 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
- Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.Journal of chemical theory and computation · 2017Article
- A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.Journal of chemical theory and computation · 2017Article
- Numerical interpretation of molecular surface field in dielectric modeling of solvation.Journal of computational chemistry · 2017Article
- 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
- Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 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
- Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State.Structure (London, England : 1993) · 2015Article
- Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.Journal of theoretical & computational chemistry · 2014Article
- A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.Computer physics communications · 2014Article
- Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.Computational & theoretical chemistry · 2013Article
- Electrostatic forces in the Poisson-Boltzmann systems.The Journal of chemical physics · 2013Article
- Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding.Molecular based mathematical biology · 2013Article
- Progress in developing Poisson-Boltzmann equation solvers.Molecular based mathematical biology · 2013Article
- Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications.Physical chemistry chemical physics : PCCP · 2013Article
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3 authors.
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Abstract
In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy.
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