Recent development and application of constant pH molecular dynamics (Q34300732)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25309035 AND SRC:MED&resulttype=core&format=json

21 February 2020

title

Recent development and application of constant pH molecular dynamics (English)

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21 February 2020

2

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21 February 2020

author name string

Wei Chen

series ordinal

1

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21 February 2020

Chuanyin Shi

series ordinal

3

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21 February 2020

Jana K Shen

series ordinal

4

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21 February 2020

publication date

1 January 2014

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21 February 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25309035 AND SRC:MED&resulttype=core&format=json

21 February 2020

volume

40

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21 February 2020

issue

10-11

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25309035 AND SRC:MED&resulttype=core&format=json

21 February 2020

page(s)

830-838

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25309035 AND SRC:MED&resulttype=core&format=json

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

21 February 2020

cites work

1 reference

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

6 July 2018

1 reference

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Deconstructing activation events in rhodopsin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

The pH-triggered conversion of the PrP(c) to PrP(sc.).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids

6 July 2018

1 reference

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pH-dependent dynamics of complex RNA macromolecules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

6 July 2018

1 reference

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Chaperone activation by unfolding

6 July 2018

1 reference

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pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability

6 July 2018

1 reference

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pKa determination of histidine residues in α-conotoxin MII peptides by 1H NMR and constant pH molecular dynamics simulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Structural basis for proton conduction and inhibition by the influenza M2 protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Unraveling A Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Reversibility of prion misfolding: insights from constant-pH molecular dynamics simulations.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

H 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Fine-Tuning the pH Trigger of Self-Assembly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Effects of two solvent conditions on the free energy landscape of the BBL peripheral subunit binding domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Multisite λ Dynamics for Simulated Structure–Activity Relationship Studies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Probing pH-Dependent Dissociation of HdeA Dimers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Progress in the prediction of pKa values in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

pH replica‐exchange method based on discrete protonation states

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Predicting pKa Values with Continuous Constant pH Molecular Dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Large shifts in pK a values of lysine residues buried inside a protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Essentials for ATP synthesis by F1F0 ATP synthases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

CHARMM: the biomolecular simulation program

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

High tolerance for ionizable residues in the hydrophobic interior of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Multidrug efflux transporter, AcrB--the pumping mechanism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Recent advances in implicit solvent-based methods for biomolecular simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

GROMACS: fast, flexible, and free

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Constant pH molecular dynamics with proton tautomerism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

Biomolecular simulations at constant pH.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

LINKED FUNCTIONS AND RECIPROCAL EFFECTS IN HEMOGLOBIN: A SECOND LOOK.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

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

6 July 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

Constant pH molecular dynamics in generalized Born implicit solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

Evidence for a catalytic dyad in the active site of homocitrate synthase from Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

Conformational study of GSH and GSSG using constant-pH molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

Harmonic Fourier beads method for studying rare events on rugged energy surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

The N-terminal domains of spider silk proteins assemble ultrafast and protected from charge screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4188395

28 October 2018

https://api.crossref.org/works/10.1080/08927022.2014.907492

Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/08927022.2014.907492

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

21 January 2018

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

Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein

1 reference

12 December 2020

10.1080/08927022.2014.907492

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25309035 AND SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25309035 AND SRC:MED&resulttype=core&format=json

21 February 2020

PubMed publication ID

25309035

1 reference