Differential geometry based solvation model I: Eulerian formulation (Q34183931)

31 July 2017

Differential geometry based solvation model I: Eulerian formulation (English)

1 reference

31 July 2017

2

1 reference

31 July 2017

Zhan Chen

1

1 reference

PubMed ID

20938489

31 July 2017

G W Wei

series ordinal

3

1 reference

31 July 2017

1 November 2010

1 reference

Journal of Computational Physics

31 July 2017

1 reference

31 July 2017

229

1 reference

31 July 2017

8231-8258

1 reference

31 July 2017

22

1 reference

PubMed ID

20938489

maintained by WikiProject

31 July 2017

WikiProject Mathematics

0 references

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Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications

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5 July 2018

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Electrostatic contributions to the stability of the GCN4 leucine zipper structure

5 July 2018

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Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory

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Electrostatic polarization is crucial for reproducing pKa shifts of carboxylic residues in Turkey ovomucoid third domain.

5 July 2018

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Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations

5 July 2018

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Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models

5 July 2018

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Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies

5 July 2018

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Modeling electrostatic effects in proteins

5 July 2018

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Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?

5 July 2018

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5 July 2018

Implicit solvent models

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Electrostatic contribution to the binding stability of protein-protein complexes.

5 July 2018

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PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics

5 July 2018

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5 July 2018

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Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions

5 July 2018

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5 July 2018

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Very fast empirical prediction and rationalization of protein pKa values

5 July 2018

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Improving implicit solvent simulations: a Poisson-centric view

5 July 2018

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Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte.

5 July 2018

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Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods

5 July 2018

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

5 July 2018

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An efficient hybrid explicit/implicit solvent method for biomolecular simulations

5 July 2018

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Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis

5 July 2018

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

5 July 2018

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Finite element solution of the steady-state Smoluchowski equation for rate constant calculations

5 July 2018

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GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences

5 July 2018

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Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

5 July 2018

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

5 July 2018

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Force fields for protein simulations

5 July 2018

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On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

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

5 July 2018

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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Thermodynamics and kinetics of actin filament nucleation.

5 July 2018

1 reference

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Macromolecular electrostatics: continuum models and their growing pains

5 July 2018

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Generalized born models of macromolecular solvation effects

5 July 2018

1 reference

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Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry

5 July 2018

1 reference

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Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Brownian dynamics simulation of protein-protein diffusional encounter

5 July 2018

1 reference

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The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

5 July 2018

1 reference

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Classical electrostatics in biology and chemistry

5 July 2018

1 reference

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A continuum model for protein-protein interactions: application to the docking problem.

5 July 2018

1 reference

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The interpretation of protein structures: Estimation of static accessibility

5 July 2018

1 reference

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Hydrophobic effect in protein folding and other noncovalent processes involving proteins

5 July 2018

1 reference

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pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

22 Diffusion-controlled enzymatic reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Areas, volumes, packing and protein structure

5 July 2018

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Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Geometric and potential driving formation and evolution of biomolecular surfaces.

28 October 2018

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Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Anisotropic diffusion of multivalued images with applications to color filtering.

28 October 2018

1 reference

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A computational algorithm for minimizing total variation in image restoration.

28 October 2018

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A general framework for low level vision

28 October 2018

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Color TV: total variation methods for restoration of vector-valued images

28 October 2018

1 reference

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Implicit nonpolar solvent models

28 October 2018

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The Gaussian Generalized Born model: application to small molecules.

28 October 2018

1 reference

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Treatment of charge singularities in implicit solvent models.

28 October 2018

1 reference

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Application of the level-set method to the implicit solvation of nonpolar molecules

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Treatment of geometric singularities in implicit solvent models.

28 October 2018

1 reference

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Minimal molecular surfaces and their applications.

28 October 2018

1 reference

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Highly accurate biomolecular electrostatics in continuum dielectric environments.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Optimized atomic radii for protein continuum electrostatics solvation forces.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

28 October 2018

1 reference

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A new quantum method for electrostatic solvation energy of protein.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Limitations of atom-centered dielectric functions in implicit solvent models

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Coupling nonpolar and polar solvation free energies in implicit solvent models

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Specific ion effects in solutions of globular proteins: comparison between analytical models and simulation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Surfaces affect ion pairing

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Molecular mechanics PBSA ligand binding energy and interaction of Efavirenz derivatives with HIV-1 reverse transcriptase

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Cation-pi interactions in protein-protein interfaces

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

The determinants of carboxyl pKa values in turkey ovomucoid third domain

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Electrostatic effects in macromolecules: fundamental concepts and practical modeling.

28 October 2018

1 reference

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Functionally linked hydration changes in Escherichia coli aspartate transcarbamylase and its catalytic subunit.

28 October 2018

1 reference

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The determinants of pKas in proteins

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Perspective on Foundations of Solvation Modeling: The Electrostatic Contribution to the Free Energy of Solvation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2951687

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

9 December 2018

1 reference

12 December 2020

Absorption classification of oral drugs based on molecular surface properties

1 reference

12 December 2020

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations

1 reference

12 December 2020

DNA binding and bending by HMG boxes: energetic determinants of specificity

1 reference

12 December 2020

Poisson–Boltzmann Methods for Biomolecular Electrostatics

1 reference

12 December 2020

On the calculation of pKas in proteins

1 reference

12 December 2020

Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: a density functional approach

1 reference

12 December 2020

Comparative study of generalized born models: Born radii and peptide folding

1 reference

12 December 2020

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

1 reference

12 December 2020

Hybrid Hamiltonian replica exchange molecular dynamics simulation method employing the Poisson-Boltzmann model

1 reference

12 December 2020

Conservation of electrostatic properties within enzyme families and superfamilies

1 reference

12 December 2020

Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics

1 reference

12 December 2020

Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models

1 reference

12 December 2020

Improving macromolecular electrostatics calculations

1 reference

12 December 2020

10.1016/J.JCP.2010.06.036

Identifiers

DOI

1 reference

31 July 2017

journals/jcphy/ChenBW10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

31 July 2017

1 reference

PubMed ID

20938489