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Improved Boundary Element Methods for Poisson−Boltzmann Electrostatic Potential and Force Calculations

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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A fast and Space-efficient boundary element method for computing electrostatic and hydration effects in large molecules
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199703)18:4<569::aid-jcc10>3.0.co;2-bopenalex-snapshot
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
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Reduced surface: An efficient way to compute molecular surfaces
inferredcites →https://doi.org/10.1002/1097-0282(2001)60:2<124::aid-bip1008>3.0.co;2-sopenalex-snapshot
Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide
inferredcites →https://doi.org/10.1002/1521-4001(200110)81:10<651::aid-zamm651>3.0.co;2-eopenalex-snapshot
Free Terms and Compatibility Conditions for 3D Hypersingular Boundary Integral Equations
inferredcites →https://doi.org/10.1002/jcc.10195openalex-snapshot
Boundary element solution of the linear Poisson–Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
inferredcites →https://doi.org/10.1002/jcc.20000openalex-snapshot
Hybrid boundary element and finite difference method for solving the nonlinear Poisson–Boltzmann equation
inferredcites →https://doi.org/10.1002/jcc.540120507openalex-snapshot
The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations
inferredcites →https://doi.org/10.1002/jcc.540160707openalex-snapshot
The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems
inferredcites →https://doi.org/10.1016/0021-9991(91)90043-kopenalex-snapshot
The electric potential of a macromolecule in a solvent: A fundamental approach
inferredcites →https://doi.org/10.1016/0021-9991(91)90084-xopenalex-snapshot
The electric potential of a macromolecule in a solvent: A fundamental approach
inferredcites →https://doi.org/10.1016/0022-2836(85)90399-7openalex-snapshot
A new method for computing the macromolecular electric potential
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1016/s0006-3495(97)78213-4openalex-snapshot
Computation of molecular electrostatics with boundary element methods
inferredcites →https://doi.org/10.1021/j100116a025openalex-snapshot
Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
inferredcites →https://doi.org/10.1021/ja00035a003openalex-snapshot
A combined iterative and boundary-element approach for solution of the nonlinear Poisson-Boltzmann equation
inferredcites →https://doi.org/10.1021/jp013607qopenalex-snapshot
Fast Boundary Element Method for the Linear Poisson−Boltzmann Equation
inferredcites →https://doi.org/10.1021/jp962215uopenalex-snapshot
Classical Variational Transition State Theory Study of Hydrogen Atom Diffusion Dynamics in Imperfect Xenon Matrices
inferredcites →https://doi.org/10.1063/1.1924448openalex-snapshot
Computation of electrostatic forces between solvated molecules determined by the Poisson–Boltzmann equation using a boundary element method
inferredcites →https://doi.org/10.1063/1.2008252openalex-snapshot
Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals
inferredcites →https://doi.org/10.1142/9789814503860_0002openalex-snapshot
MODELING SCATTERED FUNCTION DATA ON CURVED SURFACES
inferredcites →https://doi.org/10.1145/774572.774640openalex-snapshot
Fast methods for simulation of biomolecule electrostatics
inferredcites →https://doi.org/10.1201/9781420035254openalex-snapshot
A Practical Guide to Boundary Element Methods with the Software Library BEMLIB

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Optimized Parallelization of Boundary Integral Poisson-Boltzmann Solvers
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Application of the thin‐shell formulation to the numerical modeling of Stern layer in biomolecular electrostatics
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Accuracy assessment of the linear P oisson– B oltzmann equation and reparametrization of the OBC generalized B orn model for nucleic acids and nucleic acid–protein complexes
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p K A in proteins solving the P oisson– B oltzmann equation with finite elements
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DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
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Numerical interpretation of molecular surface field in dielectric modeling of solvation
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ARGOS: An adaptive refinement goal‐oriented solver for the linearized Poisson–Boltzmann equation
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Bridging Eulerian and Lagrangian Poisson–Boltzmann solvers by ESES
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Modeling of Electrostatic Effects in Macromolecules
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Modeling of Electrostatic Effects in Macromolecules
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Advances in Implicit Models of Water Solvent to Compute Conformational Free Energy and Molecular Dynamics of Proteins at Constant pH
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AFMPB: An adaptive fast multipole Poisson–Boltzmann solver for calculating electrostatics in biomolecular systems
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Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns
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IPEC Solver: Numerical simulation tool to study inter-polyelectrolyte complexation
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Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
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Optimized parallelization of boundary integral Poisson-Boltzmann solvers
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Dielectric boundary force in numerical Poisson–Boltzmann methods: Theory and numerical strategies
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“New-version-fast-multipole-method” accelerated electrostatic calculations in biomolecular systems
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A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule
inferred← citeshttps://doi.org/10.1016/j.molliq.2023.123119openalex-snapshot
Prediction of cosolvent effect on solvation free energies and analysis of intermolecular forces of tizanidine hydrochloride in ethyl acetate + methanol / ethanol mixtures
inferred← citeshttps://doi.org/10.1021/acs.chemrev.9b00055openalex-snapshot
End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00368openalex-snapshot
Comparison Study of Polar and Nonpolar Contributions to Solvation Free Energy
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00021openalex-snapshot
Accurate Boundary Integral Formulations for the Calculation of Electrostatic Forces with an Implicit-Solvent Model
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c04604openalex-snapshot
TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver
inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b05444openalex-snapshot
Interaction between Charged Cylinders in Electrolyte Solution; Excluded Volume Effect
inferred← citeshttps://doi.org/10.1021/ct100145fopenalex-snapshot
New and Efficient Poisson−Boltzmann Solver for Interaction of Multiple Proteins
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Calculating the Bimolecular Rate of Protein–Protein Association with Interacting Crowders
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mFES: A Robust Molecular Finite Element Solver for Electrostatic Energy Computations
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An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics
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FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins
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Peptide Folding Using Multiscale Coarse-Grained Models
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Dielectric pressure in continuum electrostatic solvation of biomolecules
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Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution
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Electrostatic forces in the Poisson-Boltzmann systems
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Biomolecular electrostatics—I want your solvation (model)
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Boundary element analysis of the electrostatic interactions between organic scaffolds and transmembrane proteins
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Recent progress in adapting Poisson–Boltzmann methods to molecular simulations
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Hierarchical molecular interfaces and solvation electrostatics
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Optimized parallelization of boundary integral Poisson-Boltzmann solvers
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Error analysis of virtual element method for the Poisson–Boltzmann equation
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Progress in developing Poisson-Boltzmann equation solvers
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Adaptive Goal-Oriented Solver for the Linearized Poisson- Boltzmann Equation
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Adaptive Goal-Oriented Solver for the Linearized Poisson- Boltzmann Equation
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Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver
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DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
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DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
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