Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi (original) (raw)
Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi
Emil Alexov
Journal of Chemical Information and Modeling
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Beyond standard Poisson-Boltzmann theory: ion-specific interactions in aqueous solutions
David Andelman
Journal of Physics-condensed Matter, 2009
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Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0]
Emil Alexov
Living Journal of Computational Molecular Science
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Beyond the Poisson-Boltzmann Model: Modeling Biomolecule-Water and Water-Water Interactions
Marc Delarue, Patrice Koehl
Physical Review Letters, 2009
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Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents
Emil Alexov
Frontiers in Molecular Biosciences
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A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
Tania Hazra
Journal of Mathematical Biology, 2019
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A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential
Emil Alexov
Langmuir : the ACS journal of surfaces and colloids, 2017
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Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics
Mohamed Bon
2008
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PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics
Marc Delarue, Patrice Koehl
Nucleic Acids Research, 2006
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Modeling salt‐mediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome
Tamar Schlick
Biopolymers, 2001
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Ionic strength independence of charge distributions in solvation of biomolecules
Tobin Sosnick
The Journal of chemical physics, 2014
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BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics
Emil Alexov
International Journal of Molecular Sciences, 2020
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Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes
Emil Alexov
2019
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On the Use of Different Dielectric Constants for Computing Individual and Pairwise Terms in Poisson−Boltzmann Studies of Protein Ionization Equilibrium
Antonio Baptista
The Journal of Physical Chemistry B, 2005
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Poisson-Boltzmann Calculations of Nonspecific Salt Effects on Protein-Protein Binding Free Energies
Emil Alexov
Biophysical Journal, 2007
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BION-2: Predicting Positions of Non-Specifically Bound ions on Protein Surface by a Gaussian-based Treatment of Electrostatic Environment
Emil Alexov
2020
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Predicting Nonspecific Ion Binding Using DelPhi
Emil Alexov
Biophysical Journal, 2012
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Between algorithm and model: Different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution
Emil Alexov
Communications in Computational Physics, 2013
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Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson–Boltzmann Solvent
Matthew Knepley
Journal of Chemical Theory and Computation, 2017
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New Computational Models for Electrostatics of Macromolecules in Solvents
Igor Tsukerman
IEEE Transactions on Magnetics, 2000
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The electric potential of a macromolecule in a solvent: A fundamental approach
André Juffer
Journal of Computational Physics, 1991
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Biomolecular Electrostatics with the Linearized Poisson-Boltzmann Equation
Paolo Viglino, Gennaro Esposito
Biophysical Journal, 1999
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Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation
Michał Bosy
arXiv (Cornell University), 2023
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Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann method
Kim Sharp
Journal of Computational Chemistry, 1991
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A Nonlinear Boundary Condition for Continuum Models of Biomolecular Electrostatics
Matthew Knepley
2015
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Electrostatic potentials of proteins in water: a structured continuum approach
anhy many
Bioinformatics/computer Applications in The Biosciences, 2007
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Protein−Ion Binding Process on Finite Macromolecular Concentration. A Poisson−Boltzmann and Monte Carlo Study
Marcia Fenley
The Journal of Physical Chemistry B, 2008
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On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes
Fabrizio Cleri
Scientific reports, 2016
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Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
Alexey Onufriev
The Journal of Chemical Physics, 2006
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