Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation (Q35866766)

10 August 2017

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

1 reference

10 August 2017

Chuanyin Shi

1

1 reference

10 August 2017

Jason A Wallace

series ordinal

2

1 reference

10 August 2017

Jana K Shen

series ordinal

3

1 reference

10 August 2017

language of work or name

English

0 references

publication date

3 April 2012

1 reference

10 August 2017

1 reference

10 August 2017

102

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10 August 2017

7

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10 August 2017

1590-1597

1 reference

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

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Progress in the prediction of pKa values in proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Predicting pKa values with continuous constant pH molecular dynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

CHARMM: the biomolecular simulation program

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

High tolerance for ionizable residues in the hydrophobic interior of proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

High Apparent Dielectric Constant Inside a Protein Reflects Structural Reorganization Coupled to the Ionization of an Internal Asp

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Molecular dynamics study of water penetration in staphylococcal nuclease.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Constant pH molecular dynamics with proton tautomerism

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Stabilization of internal charges in a protein: water penetration or conformational change?

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Structural interpretation of pH and salt-dependent processes in proteins with computational methods

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

High apparent dielectric constants in the interior of a protein reflect water penetration

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Canonical dynamics: Equilibrium phase-space distributions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Macroscopic electrostatic models for protonation states in proteins

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Generalized born model with a simple smoothing function.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

Molden: a pre- and post-processing program for molecular and electronic structures.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3318114

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

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22500759

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A method to determine residue-specific unfolded-state pKa values from analysis of stability changes in single mutant cycles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22500759

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2012.02.021

1 reference

10 August 2017

1 reference

10 August 2017

PubMed publication ID

22500759

1 reference