Constant pH molecular dynamics with proton tautomerism (Q34350350)

1 August 2017

Constant pH molecular dynamics with proton tautomerism (English)

1 reference

1 August 2017

Jana Khandogin

1

1 reference

PubMed ID

15863480

1 August 2017

Charles L Brooks

series ordinal

2

1 reference

PubMed ID

15863480

1 August 2017

language of work or name

English

0 references

publication date

29 April 2005

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1 August 2017

17

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inferred from page(s)

published in

Biophysical Journal

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1 August 2017

89

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1 August 2017

1

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1 August 2017

141-157

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

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane 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=1366513

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s 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=1366513

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

The amyloid-beta peptide and its role in Alzheimer's disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Structural changes linked to proton translocation by subunit c of the ATP synthase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Protein titration in the crystal state.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Canonical dynamics: Equilibrium phase-space distributions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Amyloid fibril formation and protein misassembly: a structural quest for insights into amyloid and prion diseases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Structure of influenza haemagglutinin at the pH of membrane fusion

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

pH, ionic strength, and temperature dependences of ionization equilibria for the carboxyl groups in turkey ovomucoid third 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=1366513

pH-dependent processes 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=1366513

X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Structure of phosphate-free ribonuclease A refined at 1.26 .ANG

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

pH-dependent insertion of proteins into membranes: B-chain mutation of diphtheria toxin that inhibits membrane translocation, Glu-349----Lys

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Optimized atomic radii for protein continuum electrostatics solvation forces.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Constant pH molecular dynamics in generalized Born implicit solvent

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

The determinants of carboxyl pKa values in turkey ovomucoid third domain

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Generalized born model with a simple smoothing function.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

The determinants of pKas in proteins

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366513

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

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15863480

12 December 2020

inferred from PubMed ID database lookup

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15863480

12 December 2020

inferred from PubMed ID database lookup

His···Asp Catalytic Dyad of Ribonuclease A: Conformational Stability of the Wild-Type, D121N, D121A, and H119A Enzymes†

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15863480

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1529/BIOPHYSJ.105.061341

1 reference

1 August 2017

1 reference

1 August 2017

1 reference

PubMed ID

15863480