(Q37701323)

English

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

scientific article published on 05 February 2014

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

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

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

2

object named as

Darrin M York

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

Adrian Roitberg

3

object named as

Adrian E Roitberg

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

author name string

Jason M Swails

1

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

language of work or name

1 reference

based on heuristic

inferred from title

publication date

5 February 2014

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

Journal of Chemical Theory and Computation

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

10

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

3

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

1341-1352

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

pH-Dependent conformational changes in proteins and their effect on experimental pK(a)s: the case of Nitrophorin 4

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Progress in the prediction of pKa values in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

pH replica-exchange method based on discrete protonation states

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Improving the description of salt bridge strength and geometry in a Generalized Born model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Generalized Born model with a simple, robust molecular volume correction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Adaptations of proteins to cellular and subcellular pH

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Long-timescale molecular dynamics simulations of protein structure and function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Intracellular pH sensors: design principles and functional significance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Comparison of multiple Amber force fields and development of improved protein backbone parameters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Constant pH molecular dynamics with proton tautomerism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Simulation and modeling of nucleic acid structure, dynamics and interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Exploring protein native states and large-scale conformational changes with a modified generalized born model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Refinement of triclinic hen egg-white lysozyme at atomic resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Electrostatic effects in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 August 2017

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

6 September 2017

Alpha/gamma transitions in the B-DNA backbone

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

14 September 2017

Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

14 September 2017

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 June 2018

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 June 2018

Electrostatic forces in two lysozymes: calculations and measurements of histidine pKa values

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

23 June 2018

Acidic range titration of HEWL using a constant-pH molecular dynamics method.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

1 September 2018

Constant pH molecular dynamics in generalized Born implicit solvent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

1 September 2018

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985686

1 September 2018

Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration

1 reference

https://pubmed.ncbi.nlm.nih.gov/24803862

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/24803862

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

https://pubmed.ncbi.nlm.nih.gov/24803862

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Langevin dynamics of proteins at constant pH

1 reference

https://pubmed.ncbi.nlm.nih.gov/24803862

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?

1 reference

https://pubmed.ncbi.nlm.nih.gov/24803862

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation

1 reference

https://pubmed.ncbi.nlm.nih.gov/24803862

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/CT401042B

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

22 August 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q37701323&oldid=2176434945"