Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations (Q38112677)

29 August 2017

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations (English)

1 reference

29 August 2017

Zhenli Xu

1

1 reference

PMCID

3671632

29 August 2017

Wei Cai

series ordinal

2

1 reference

29 August 2017

1 November 2011

1 reference

29 August 2017

1 reference

29 August 2017

53

1 reference

29 August 2017

683-720

1 reference

29 August 2017

4

1 reference

PMCID

3671632

maintained by WikiProject

29 August 2017

WikiProject Mathematics

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cites work

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A Sixth-order Image Approximation to the Ionic Solvent Induced Reaction Field

6 September 2017

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6 September 2017

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An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

6 September 2017

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Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules

6 September 2017

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6 September 2017

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Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosures

6 September 2017

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The AGBNP2 Implicit Solvation Model.

6 September 2017

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Fast Spectral Collocation Method for Surface Integral Equations of Potential Problems in a Spheroid

6 September 2017

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FAST MOLECULAR SOLVATION ENERGETICS AND FORCE COMPUTATION

6 September 2017

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A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation

6 September 2017

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Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach

6 September 2017

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Electrostatic potential of point charges inside dielectric prolate spheroids

6 September 2017

1 reference

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Image charge approximations of reaction fields in solvents with arbitrary ionic strength

6 September 2017

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Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method

6 September 2017

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Fourier transform convolution integrals applied to generalized Born molecular volume

6 September 2017

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Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics

6 September 2017

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Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory

6 September 2017

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Recent advances in implicit solvent-based methods for biomolecular simulations

6 September 2017

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Extending the Fast Multipole Method for Charges inside a Dielectric Sphere in an Ionic Solvent: High Order Image Approximations for Reaction Fields

6 September 2017

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Order N algorithm for computation of electrostatic interactions in biomolecular systems

6 September 2017

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Modeling electrostatic effects in proteins

6 September 2017

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Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies

6 September 2017

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Electrostatics calculations: latest methodological advances

6 September 2017

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GROMACS: fast, flexible, and free

6 September 2017

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Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties

6 September 2017

1 reference

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Improving implicit solvent simulations: a Poisson-centric view

6 September 2017

1 reference

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Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method

6 September 2017

1 reference

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An efficient hybrid explicit/implicit solvent method for biomolecular simulations

6 September 2017

1 reference

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Influence of the solvent structure on the electrostatic interactions in proteins

6 September 2017

1 reference

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Recent advances in the development and application of implicit solvent models in biomolecule simulations

6 September 2017

1 reference

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Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

6 September 2017

1 reference

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The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Effective Born radii in the generalized Born approximation: the importance of being perfect

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Electrostatics of nanosystems: application to microtubules and the ribosome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Generalized born models of macromolecular solvation effects

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Tanford-Kirkwood electrostatics for protein modeling.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Computation of molecular electrostatics with boundary element methods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Structure and mechanism of carbonic anhydrase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Boundary element solution of macromolecular electrostatics: interaction energy between two proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Classical electrostatics in biology and chemistry

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Calculations of electrostatic interactions in biological systems and in solutions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

The interpretation of protein structures: Estimation of static accessibility

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Energetic coupling between DNA bending and base pair opening

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Free Energy Calculations for DNA Near Surfaces Using an Ellipsoidal Geometry

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Nonperiodic boundary conditions for solvated systems

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Multiple grid methods for classical molecular dynamics.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Electrostatic interactions of charged groups in an aqueous medium and their effect on the formation of the secondary structures of polypeptide chains

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

An Analytical Electrostatic Model for Salt Screened Interactions between Multiple Proteins

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Universal Solvation Model Based on the Generalized Born Approximation with Asymmetric Descreening.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Treecode algorithm for pairwise electrostatic interactions with solvent-solute polarization.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Steric effects on ac electro-osmosis in dilute electrolytes.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Analysis of integral expressions for effective Born radii.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

The Gaussian Generalized Born model: application to small molecules.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Highly accurate biomolecular electrostatics in continuum dielectric environments.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

GBr(6): a parameterization-free, accurate, analytical generalized born method.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

New-generation amber united-atom force field

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Analytical electrostatics for biomolecules: beyond the generalized Born approximation

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Coupling nonpolar and polar solvation free energies in implicit solvent models

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Incorporating variable dielectric environments into the generalized Born model

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Implicit solvation based on generalized Born theory in different dielectric environments.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Generalized born model with a simple smoothing function.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Long-Range Electrostatic Attractions between Identically Charged Particles in Confined Geometries: An Unresolved Problem.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671632

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 October 2018

1 reference

12 December 2020

Intricate coupling between ion-ion and ion-surface correlations in double layers as illustrated by charge inversion-combined effects of strong Coulomb correlations and excluded volume

1 reference

12 December 2020

All-atom fast protein folding simulations: the villin headpiece

1 reference

12 December 2020

Dielectric response of a polar fluid trapped in a spherical nanocavity

1 reference

12 December 2020

Identifiers

DOI

10.1137/090774288

1 reference

29 August 2017

journals/siamrev/XuC11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

29 August 2017

1 reference

PMCID

3671632