Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models (Q27317289)

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English	Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models	scientific article (publication date: October 2015)

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instance of

scholarly article

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title

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models (English)

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author name string

Hyuntae Na

series ordinal

1

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Robert L Jernigan

series ordinal

2

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Guang Song

series ordinal

3

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language of work or name

English

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publication date

October 2015

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published in

PLOS Computational Biology

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volume

11

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issue

10

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page(s)

e1004542

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copyright license

Creative Commons Attribution 4.0 International

start time

16 October 2015

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

ATP-bound states of GroEL captured by cryo-electron microscopy

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

21 March 2017

The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

21 March 2017

VMD: visual molecular dynamics

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

21 March 2017

Dynamics of folded proteins

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

21 March 2017

Dynamic personalities of proteins

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

7 April 2017

Atomic torsional modal analysis for high-resolution proteins

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Real-time observation of multiple-protein complex formation with single-molecule FRET

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Generalized spring tensor models for protein fluctuation dynamics and conformation changes

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Global motions of the nuclear pore complex: insights from elastic network models

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

New tools provide new insights in NMR studies of protein dynamics

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Comparison of mode analyses at different resolutions applied to nucleic acid systems

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

The role of shape in determining molecular motions

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Protein structural transitions and their functional role

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

New advances in normal mode analysis of supermolecular complexes and applications to structural refinement

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Molecular dynamics simulations of biomolecules

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Anisotropy of fluctuation dynamics of proteins with an elastic network model

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Dynamics of a small globular protein in terms of low-frequency vibrational modes

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

Computer simulation of protein folding

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 September 2017

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

31 May 2018

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

31 May 2018

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

31 May 2018

Conformational change of proteins arising from normal mode calculations

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

31 May 2018

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

31 May 2018

The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

31 May 2018

Multiple unfolding pathways of leucine binding protein (LBP) probed by single-molecule force spectroscopy (SMFS).

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

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

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Analysis of domain motions by approximate normal mode calculations

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Molecular mechanisms of chaperonin GroEL-GroES function

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Global ribosome motions revealed with elastic network model

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Loop motions of triosephosphate isomerase observed with elastic networks.

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Conventional NMA as a better standard for evaluating elastic network models

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Reducing the bandwidth of sparse symmetric matrices

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

Bridging between normal mode analysis and elastic network models

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004542

retrieved

21 January 2018

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 November 2018

Building-block approach for determining low-frequency normal modes of macromolecules.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608564

retrieved

28 November 2018

Analysis of domain motions in large proteins

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/26473491

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/26473491

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/26473491

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A multiscale coarse-graining method for biomolecular systems

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/26473491

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Coarse-graining of protein structures for the normal mode studies

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/26473491

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004542

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

598296

DBLP publication ID

journals/ploscb/NaJS15

1 reference

stated in

DBLP Dataset 2021-01-02

retrieved

28 January 2021

OpenCitations bibliographic resource ID

598296

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

598296

PMC publication ID

4608564

0 references

PubMed publication ID

26473491

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ResearchGate publication ID

282910711

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