(Q29394790)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

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

2 references

14 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

molecular dynamics simulation

1 March 2020

main subject

0 references

author name string

Jason A Wallace

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Jana K Shen

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

publication date

1 July 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

1 March 2020

published in

2 references

14 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

volume

7

2 references

14 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

issue

8

2 references

14 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

page(s)

2617-2629

2 references

14 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

pKaValues and the pH Dependent Stability of the N-Terminal Domain of L9 as Probes of Electrostatic Interactions in the Denatured State. Differentiation between Local and Nonlocal Interactions†

1 March 2020

cites work

1 reference

12 December 2020

Electrostatic aspects of protein-protein interactions.

1 reference

12 December 2020

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

1 reference

12 December 2020

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

1 reference

12 December 2020

Calculating pKa values in enzyme active sites

1 reference

12 December 2020

Generalized born model with a simple smoothing function.

1 reference

12 December 2020

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

1 reference

12 December 2020

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations

1 reference

12 December 2020

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

1 reference

12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

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

1 reference

12 December 2020

Constant pH molecular dynamics in generalized Born implicit solvent

1 reference

12 December 2020

Biomolecular simulations at constant pH.

1 reference

12 December 2020

Constant pH molecular dynamics with proton tautomerism

1 reference

12 December 2020

Molecular dynamics study of water penetration in staphylococcal nuclease.

1 reference

12 December 2020

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

1 reference

12 December 2020

pK values of the ionizable groups of proteins

1 reference

12 December 2020

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

1 reference

12 December 2020

Exploring atomistic details of pH-dependent peptide folding

1 reference

12 December 2020

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

1 reference

12 December 2020

Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network

1 reference

12 December 2020

Generalized ensemble and tempering simulations: a unified view.

1 reference

12 December 2020

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

1 reference

12 December 2020

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

1 reference

12 December 2020

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

1 reference

12 December 2020

Optimized explicit-solvent replica exchange molecular dynamics from scratch.

1 reference

12 December 2020

Downhill versus barrier-limited folding of BBL 1: energetic and structural perturbation effects upon protonation of a histidine of unusually low pKa.

1 reference

12 December 2020

CHARMM: the biomolecular simulation program

1 reference

12 December 2020

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

1 reference

12 December 2020

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

1 reference

12 December 2020

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

1 reference

12 December 2020

Probing the strand orientation and registry alignment in the propagation of amyloid fibrils

1 reference

12 December 2020

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

1 reference

12 December 2020

Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

1 reference

12 December 2020

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

1 reference

12 December 2020

Predicting pKa values with continuous constant pH molecular dynamics

1 reference

12 December 2020

Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models

1 reference

12 December 2020

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

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

Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Canonical dynamics: Equilibrium phase-space distributions

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT200146J

3 references

14 April 2017

Consolidated OpenCitations Corpus – April 2017

3121436

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

3121436

1 reference

Consolidated OpenCitations Corpus – April 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

PubMed publication ID

26606635

2 references

Consolidated OpenCitations Corpus – April 2017

3121436

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26606635%20AND%20SRC:MED&resulttype=core&format=json