(Q37055280)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23638941%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

title

NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations (English)

1 reference

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29 February 2020

1

1 reference

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29 February 2020

author name string

Nan-jie Deng

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23638941%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Ronald M Levy

series ordinal

3

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29 February 2020

language of work or name

English

0 references

publication date

28 May 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23638941%20AND%20SRC:MED&resulttype=core&format=json

Journal of Physical Chemistry B

29 February 2020

published in

1 reference

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29 February 2020

volume

117

1 reference

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29 February 2020

issue

22

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23638941%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

page(s)

6625-6634

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23638941%20AND%20SRC:MED&resulttype=core&format=json

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

29 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation.

29 September 2017

1 reference

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Coupling between internal dynamics and rotational diffusion in the presence of exchange between discrete molecular conformations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Sucrose in aqueous solution revisited, Part 1: molecular dynamics simulations and direct and indirect dipolar coupling analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Everything you wanted to know about Markov State Models but were afraid to ask

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

The AGBNP2 Implicit Solvation Model.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

The role of dynamic conformational ensembles in biomolecular recognition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Influence of the coupling of interdomain and overall motions on NMR relaxation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Transition networks for modeling the kinetics of conformational change in macromolecules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Evaluating rotational diffusion from protein MD simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Simulating replica exchange simulations of protein folding with a kinetic network model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

A model of interdomain mobility in a multidomain protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Targeting structural flexibility in HIV-1 protease inhibitor binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

An NMR perspective on enzyme dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Protein folding pathways from replica exchange simulations and a kinetic network model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Combined effect of restricted rotational diffusion plus jumps on nuclear magnetic resonance and fluorescence probes of aromatic ring motions in proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

"Wide-open" 1.3 A structure of a multidrug-resistant HIV-1 protease as a drug target

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Markov models of molecular kinetics: generation and validation

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Drug pressure selected mutations in HIV-1 protease alter flap conformations

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Probability distributions of molecular observables computed from Markov models.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Coarse master equations for peptide folding dynamics.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Temperature weighted histogram analysis method, replica exchange, and transition paths.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

HIVdb: a database of the structures of human immunodeficiency virus protease

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Flexibility and function in HIV-1 protease

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727231

Theory and applications of the generalized Born solvation model in macromolecular simulations

4 December 2018

1 reference

12 December 2020

Crucial roles of the subnanosecond local dynamics of the flap tips in the global conformational changes of HIV-1 protease

1 reference

12 December 2020

NMR characterization of the dynamics of biomacromolecules

1 reference

12 December 2020

Monitoring inhibitor-induced conformational population shifts in HIV-1 protease by pulsed EPR spectroscopy

1 reference

12 December 2020

Interflap distances in HIV-1 protease determined by pulsed EPR measurements

1 reference

12 December 2020

General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation

1 reference

12 December 2020

Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function

1 reference

12 December 2020

Solvation influences flap collapse in HIV-1 protease

1 reference

12 December 2020

Anisotropic rotational diffusion of perdeuterated HIV protease from 15N NMR relaxation measurements at two magnetic fields

1 reference

12 December 2020

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP400797Y

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23638941%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23638941%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

PubMed publication ID

23638941

1 reference