Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. (Q47617147)

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9 April 2020

title

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems (English)

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9 April 2020

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9 April 2020

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9 April 2020

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9 April 2020

James C Phillips

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9 April 2020

Donghyuk Suh

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9 April 2020

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Sunhwan Jo

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9 April 2020

Wei Jiang

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9 April 2020

Klaus Schulten

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publication date

22 November 2017

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Journal of Chemical Theory and Computation

9 April 2020

published in

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volume

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issue

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9 April 2020

page(s)

5933-5944

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Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations.

9 April 2020

cites work

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Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

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pH-dependent dynamics of complex RNA macromolecules

29 September 2018

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Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

29 September 2018

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pH-replica exchange molecular dynamics in proteins using a discrete protonation method

29 September 2018

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Biomolecular simulation: a computational microscope for molecular biology

29 September 2018

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Theory of binless multi-state free energy estimation with applications to protein-ligand binding

29 September 2018

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Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing

29 September 2018

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Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

29 September 2018

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Dysregulated pH: a perfect storm for cancer progression.

29 September 2018

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Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

29 September 2018

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Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

29 September 2018

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CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes

29 September 2018

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Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease

29 September 2018

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A summary of the measured pK values of the ionizable groups in folded proteins

29 September 2018

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Statistically optimal analysis of samples from multiple equilibrium states

29 September 2018

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pK values of the ionizable groups of proteins

29 September 2018

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29 September 2018

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29 September 2018

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Constant pH molecular dynamics with proton tautomerism

29 September 2018

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Biomolecular simulations at constant pH.

29 September 2018

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29 September 2018

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29 September 2018

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29 September 2018

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Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines

29 September 2018

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1H-NMR study on the tautomerism of the imidazole ring of histidine residues. I. Microscopic pK values and molar ratios of tautomers in histidine-containing peptides

29 September 2018

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Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations

29 September 2018

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An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

1 December 2018

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Molecular simulation with variable protonation states at constant pH

1 December 2018

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12 December 2020

CHARMM-GUI: a web-based graphical user interface for CHARMM

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12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

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12 December 2020

pK(a) Values of Titrable Amino Acids at the Water/Membrane Interface

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12 December 2020

Intrinsic Dissociation Constants of Aspartyl and Glutamyl Carboxyl Groups

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12 December 2020

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

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12 December 2020

Identifiers

DOI

10.1021/ACS.JCTC.7B00875

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9 April 2020

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9 April 2020

PubMed publication ID

29111720

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