(Q36156755)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

title

Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

3

1 reference

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9 January 2020

author name string

Bin W Zhang

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

David Jasnow

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

language of work or name

English

0 references

publication date

1 November 2007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

9 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

volume

104

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

page(s)

18043-18048

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

issue

46

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

Conformational transitions of adenylate kinase: switching by cracking

9 January 2020

cites work

1 reference

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Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

2 October 2017

1 reference

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Microsecond time scale rotation measurements of single F1-ATPase molecules

2 October 2017

1 reference

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iGNM: a database of protein functional motions based on Gaussian Network Model.

2 October 2017

1 reference

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Long-timescale simulation methods

2 October 2017

1 reference

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Theory of protein folding

2 October 2017

1 reference

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Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing

2 October 2017

1 reference

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Transition-path sampling of β-hairpin folding

2 October 2017

1 reference

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The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation

2 October 2017

1 reference

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Steered molecular dynamics and mechanical functions of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Bimolecular reaction simulation using Weighted Ensemble Brownian dynamics and the University of Houston Brownian Dynamics program

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Calmodulin: a prototypical calcium sensor

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Effect of denaturant and protein concentrations upon protein refolding and aggregation: a simple lattice model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Folding thermodynamics of a model three-helix-bundle protein.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Weighted-ensemble Brownian dynamics simulations for protein association reactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Principles of protein folding--a perspective from simple exact models.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Computer simulation of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Respective roles of short- and long-range interactions in protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Supersymmetric Langevin equation to explore free-energy landscapes.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Transition-event durations in one-dimensional activated processes.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Resolution exchange simulation.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Simulating rare events in equilibrium or nonequilibrium stochastic systems.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

A doubly nudged elastic band method for finding transition states.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Computing time scales from reaction coordinates by milestoning.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Computing the transition state populations in simple protein models.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Efficient dynamic importance sampling of rare events in one dimension.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Conformational transitions using molecular dynamics with minimum biasing.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2084293

Gaussian Dynamics of Folded Proteins

23 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706349104

Resolution Exchange Simulation with Incremental Coarsening.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706349104

Predicting slow structural transitions in macromolecular systems: Conformational flooding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706349104

Reaction-rate theory: fifty years after Kramers

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706349104

Sampling small-scale and large-scale conformational changes in proteins and molecular complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706349104

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/10.1073%2FPNAS.0706349104

Backbone dynamics and energetics of a calmodulin domain mutant exchanging between closed and open conformations

21 January 2018

1 reference

12 December 2020

The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation

1 reference

12 December 2020

Using motion planning to study protein folding pathways

1 reference

12 December 2020

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

1 reference

12 December 2020

A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0706349104

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

0 references

release_2g52vrzo6zhpdi3gkwfbsxtcpq

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/2g52vrzo6zhpdi3gkwfbsxtcpq

24 November 2022

mapped directly with Wikidata item

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17984047%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

1 reference