ArticleJournal of computational chemistry2015
Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 8 citations in OpenAlex.
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- Insights into DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.Journal of chemical theory and computation · 2018Article
- Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.Scientific reports · 2016Article
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Authors and funding
4 authors at 4 institutions in 1 country.
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Abstract
The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf ) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson-Boltzmann equation solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software.
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