Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics (Q34195265)

31 July 2017

title

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics (English)

1 reference

31 July 2017

Wei Chen

1

1 reference

31 July 2017

Jana K Shen

series ordinal

2

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31 July 2017

publication date

21 August 2014

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Journal of Computational Chemistry

31 July 2017

published in

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31 July 2017

volume

35

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31 July 2017

issue

27

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31 July 2017

page(s)

1986-1996

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Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

All-atom empirical potential for molecular modeling and dynamics studies of proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

pH-dependent dynamics of complex RNA macromolecules

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

pH replica‐exchange method based on discrete protonation states

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Predicting pKa Values with Continuous Constant pH Molecular Dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

CHARMM: the biomolecular simulation program

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Exploring atomistic details of pH-dependent peptide folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Toward the accurate first-principles prediction of ionization equilibria in proteins.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Constant pH molecular dynamics with proton tautomerism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Canonical dynamics: Equilibrium phase-space distributions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Cutoff size does strongly influence molecular dynamics results on solvated polypeptides

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165709

Recent development and application of constant pH molecular dynamics

28 July 2018

1 reference

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

21 January 2018

1 reference

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model.

21 January 2018

1 reference

Introducing titratable water to all-atom molecular dynamics at constant pH.

21 January 2018

1 reference

Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions

21 January 2018

1 reference

Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method.

21 January 2018

1 reference

Free Energy of Ionic Hydration

21 January 2018

1 reference

Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels

21 January 2018

1 reference

The Origin of Layer Structure Artifacts in Simulations of Liquid Water

21 January 2018

1 reference

12 December 2020

Potentials of mean force between ionizable amino acid side chains in water

1 reference

12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

Simulating pH titration of a single surfactant in ionic and nonionic surfactant micelles

1 reference

12 December 2020

Incorporating the effect of ionic strength in free energy calculations using explicit ions

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.23713

1 reference

31 July 2017

1 reference

DBLP Dataset 2021-01-02

release_7p3b3unhjbe7fl5mqrff4xnnuy

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/7p3b3unhjbe7fl5mqrff4xnnuy

24 November 2022

mapped directly with Wikidata item

PMC publication ID

4165709

1 reference

31 July 2017

1 reference