(Q37340971)

19 August 2017

pH-replica exchange molecular dynamics in proteins using a discrete protonation method (English)

1 reference

19 August 2017

3

Adrian E Roitberg

1 reference

19 August 2017

Danial Sabri Dashti

1

1 reference

19 August 2017

Yilin Meng

series ordinal

2

1 reference

19 August 2017

language of work or name

English

0 references

publication date

17 July 2012

1 reference

Journal of Physical Chemistry B

19 August 2017

1 reference

19 August 2017

116

1 reference

19 August 2017

30

1 reference

19 August 2017

8805-8811

1 reference

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

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

pH replica-exchange method based on discrete protonation states

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Accurate, conformation-dependent predictions of solvent effects on protein ionization constants

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Exploring atomistic details of pH-dependent peptide folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Comparison of multiple Amber force fields and development of improved protein backbone parameters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Constant pH molecular dynamics with proton tautomerism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Biomolecular simulations at constant pH.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Escaping free-energy minima

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Generalized-ensemble algorithms for molecular simulations of biopolymers

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Electrostatic contributions to molecular free energies in solution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Determinants of ligand binding to cAMP-dependent protein kinase.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Constant pH molecular dynamics in generalized Born implicit solvent

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3839795

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

20 October 2018

1 reference

12 December 2020

Exchange frequency in replica exchange molecular dynamics

1 reference

12 December 2020

Information theoretical measures to analyze trajectories in rational molecular design

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/JP303385X

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

22694266

1 reference