ArticleJournal of chemical theory and computation2010
A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Engineering unnatural cells with a 21st amino acid as a living epigenetic sensor.Nature communications · 2025Article
- Charge-Induced Polarization in Dielectric Particle Systems: A Geometry-Dependent Effect.Journal of chemical theory and computation · 2025Article
- Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson-Boltzmann Framework: An Analytical Treatment.The journal of physical chemistry. B · 2022Article
- Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association.Biomolecules · 2020Article
- Improvements to the APBS biomolecular solvation software suite.Protein science : a publication of the Protein Society · 2018Article
- PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.Journal of computational chemistry · 2017Article
- Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.Scientific reports · 2017Article
- Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications.Physical chemistry chemical physics : PCCP · 2013Article
- Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.Chemical physics letters · 2013Article
- Enumerating pathways of proton abstraction based on a spatial and electrostatic analysis of residues in the catalytic site.PloS one · 2012Article
- Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.SIAM review. Society for Industrial and Applied Mathematics · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We derive a new numerical approach to solving the linearized Poisson Boltzmann equation (PBE) by representing the protein surface as a collection of spheres in which the surface charges can then be iteratively solved by new analytical multipole methods previously introduced by us [Lotan & Head-Gordon, 2006]. We show that our Poisson Boltzmann semi-analytical method, PB-SAM, realizes better accuracy, more flexible memory management, and at reduced cost relative to either finite difference or boundary element method PBE solvers. We provide two new benchmarks of PBE solution accuracy to test the numerical PBE solutions based on (1) arrays of up to hundreds of spherical low dielectric geometries with asymmetric charges in which mutual polarization is treated exactly, and (2) two overlapping spheres with increasing charge asymmetry by solving the PB-SAM method to very high pole order. We illustrate the strength of the PB-SAM approach by computing the potential profile of an array of 60 T1-particle forming monomers of the bromine mosaic virus.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.