(Q42035856)

15 October 2017

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics (English)

1 reference

15 October 2017

3

J Andrew McCammon

1 reference

15 October 2017

Sarah L Williams

1

1 reference

PMCID

2817915

15 October 2017

César Augusto F de Oliveira

series ordinal

2

1 reference

15 October 2017

14 January 2010

1 reference

Journal of Chemical Theory and Computation

15 October 2017

1 reference

15 October 2017

6

1 reference

15 October 2017

2

1 reference

15 October 2017

560-568

1 reference

Recent advances in implicit solvent-based methods for biomolecular simulations

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Rapid and simple protein-stability screens: application to membrane proteins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

GROMACS: fast, flexible, and free

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Constant pH molecular dynamics with proton tautomerism

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Biomolecular simulations at constant pH.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Effective Born radii in the generalized Born approximation: the importance of being perfect

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Explicit solvent models in protein pKa calculations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Prediction of pH-dependent properties of proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Constant pH molecular dynamics in generalized Born implicit solvent

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Macroscopic electrostatic models for protonation states in proteins

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Generalized born model with a simple smoothing function.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

On the pH dependence of protein stability.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817915

Energy landscape of a small peptide revealed by dihedral angle principal component analysis

17 August 2018

1 reference

12 December 2020

Molecular simulation with variable protonation states at constant pH

1 reference

12 December 2020

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

1 reference

12 December 2020

Interpretation of protein titration curves. Application to lysozyme

1 reference

12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT9005294

1 reference

15 October 2017

1 reference

15 October 2017

1 reference

PMCID

2817915