(Q27322857)

1

0 references

Mert Gur

2

0 references

Mary Hongying Cheng

3

0 references

Sunhwan Jo

4

0 references

Benoît Roux

PLOS Computational Biology

6

0 references

language of work or name

English

0 references

publication date

April 2014

0 references

published in

0 references

volume

10

0 references

issue

4

0 references

page(s)

e1003521

0 references

copyright license

Creative Commons Attribution 4.0 International

start time

3 April 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Minimum free energy path of ligand-induced transition in adenylate kinase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Crystal structure of an asymmetric trimer of a bacterial glutamate transporter homolog

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

X-ray structures of LeuT in substrate-free outward-open and apo inward-open states

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Many local motions cooperate to produce the adenylate kinase conformational transition

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Transport mechanism of a bacterial homologue of glutamate transporters.

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Intrinsic motions along an enzymatic reaction trajectory

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Conformational transitions of adenylate kinase: switching by cracking

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Atomic-level characterization of the activation mechanism of SERCA by calcium

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Interconversion of functional motions between mesophilic and thermophilic adenylate kinases

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Structure of a glutamate transporter homologue from Pyrococcus horikoshii

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT.

24 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Intracellular gating in an inward-facing state of aspartate transporter Glt(Ph) is regulated by the movements of the helical hairpin HP2

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Intermediate state trapping of a voltage sensor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: on-the-fly string method calculations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Simulations of the alternating access mechanism of the sodium symporter Mhp1.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Large collective motions regulate the functional properties of glutamate transporter trimers

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Global dynamics of proteins: bridging between structure and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Gating transition of pentameric ligand-gated ion channels

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Segmented transition pathway of the signaling protein nitrogen regulatory protein C

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

How Ca2+-ATPase pumps ions across the sarcoplasmic reticulum membrane

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Iterative cluster-NMA: A tool for generating conformational transitions in proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Structural aspects of ion pumping by Ca2+-ATPase of sarcoplasmic reticulum

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Src kinase conformational activation: thermodynamics, pathways, and mechanisms

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Interdomain fluorescence resonance energy transfer in SERCA probed by cyan-fluorescent protein fused to the actuator domain.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Finding transition pathways using the string method with swarms of trajectories

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Coarse-grained free energy functions for studying protein conformational changes: a double-well network model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Coarse-grained normal mode analysis in structural biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Long-timescale simulation methods

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Phosphoryl transfer and calcium ion occlusion in the calcium pump

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Escaping free-energy minima

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Efficient generation of feasible pathways for protein conformational transitions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Anisotropy of fluctuation dynamics of proteins with an elastic network model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Weighted-ensemble Brownian dynamics simulations for protein association reactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Steady-state simulations using weighted ensemble path sampling

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Rigid-cluster models of conformational transitions in macromolecular machines and assemblies

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Conformational change of proteins arising from normal mode calculations

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Anton, a special-purpose machine for molecular dynamics simulation

31 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

String method in collective variables: minimum free energy paths and isocommittor surfaces.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Cholesterol flip-flop: insights from free energy simulation studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Computing ensembles of transitions from stable states: Dynamic importance sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Predicting slow structural transitions in macromolecular systems: Conformational flooding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Geometry-based sampling of conformational transitions in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Protein conformational transitions explored by mixed elastic network models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Noninteracting local‐structure model of folding and unfolding transition in globular proteins. II. Application to two‐dimensional lattice proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Conformational transitions in adenylate kinase. Allosteric communication reduces misligation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Simplified and improved string method for computing the minimum energy paths in barrier-crossing events.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003521

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974643

Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24699246

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Multiple state transition interface sampling of alanine dipeptide in explicit solvent

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24699246

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Elastic models of conformational transitions in macromolecules

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24699246

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003521

1 reference

journals/ploscb/DasGCJBR14

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

PubMed publication ID

24699246

1 reference