(Q33880577)

29 July 2017

title

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

1 reference

29 July 2017

2

Adrian E Roitberg

1 reference

29 July 2017

Yilin Meng

1

1 reference

29 July 2017

publication date

1 April 2010

1 reference

Journal of Chemical Theory and Computation

29 July 2017

published in

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29 July 2017

volume

6

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29 July 2017

issue

4

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29 July 2017

page(s)

1401-1412

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Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

29 July 2017

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations

5 July 2018

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

5 July 2018

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

5 July 2018

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Structural basis of perturbed pKa values of catalytic groups in enzyme active sites

5 July 2018

1 reference

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Generalized-ensemble algorithms for molecular simulations of biopolymers

5 July 2018

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Generalized born models of macromolecular solvation effects

5 July 2018

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Protonation states and pH titration in the photocycle of photoactive yellow protein

5 July 2018

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Multicanonical ensemble: A new approach to simulate first-order phase transitions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Determinants of ligand binding to cAMP-dependent protein kinase.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Calculations of electrostatic interactions and pKas in the active site of Escherichia coli thioredoxin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Electrostatic contributions to molecular free energies in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects

5 July 2018

1 reference

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Alternative conformations of amyloidogenic proteins govern their behavior

5 July 2018

1 reference

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Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines

5 July 2018

1 reference

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Prediction of pH-dependent properties of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

pH-dependent processes in proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Nature of the charged-group effect on the stability of the C-peptide helix

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Evaluation of catalytic free energies in genetically modified proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Electrostatic Energy and Macromolecular Function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Elucidating the Conformational Dependence of Calculated pKa Values

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Molecular dynamics at constant pH and reduction potential: application to cytochrome c(3)

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Constant pH molecular dynamics in generalized Born implicit solvent

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

The determinants of pKas in proteins

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

On the pH dependence of protein stability.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877402

Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir

29 October 2018

1 reference

12 December 2020

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

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

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

Langevin dynamics of proteins at constant pH

1 reference

12 December 2020

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study

1 reference

12 December 2020

What about protein polarity?

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT900676B

1 reference

29 July 2017

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29 July 2017

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