How well can we understand large-scale protein motions using normal modes of elastic network models? (Q41884486)

13 October 2017

How well can we understand large-scale protein motions using normal modes of elastic network models? (English)

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13 October 2017

Robert L Jernigan

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13 October 2017

Lei Yang

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13 October 2017

Guang Song

series ordinal

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13 October 2017

language of work or name

English

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publication date

4 May 2007

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13 October 2017

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inferred from page(s)

published in

Biophysical Journal

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13 October 2017

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13 October 2017

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13 October 2017

920-929

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Atom-by-atom analysis of global downhill protein folding

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

The Database of Macromolecular Motions: new features added at the decade mark

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Dynamics of proteins in crystals: comparison of experiment with simple models

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Conformational change of proteins arising from normal mode calculations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Anisotropy of fluctuation dynamics of proteins with an elastic network model

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

A database of macromolecular motions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Rigid domains in proteins: an algorithmic approach to their identification

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Dynamics of folded proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Automatic domain decomposition of proteins by a Gaussian Network Model.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Global ribosome motions revealed with elastic network model

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Protein flexibility predictions using graph theory

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Analysis of domain motions by approximate normal mode calculations

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Hinge-bending motion in citrate synthase arising from normal mode calculations.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913142

Proteins downhill all the way

2 December 2018

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12 December 2020

Analysis of domain motions in large proteins

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12 December 2020

An enhanced elastic network model to represent the motions of domain-swapped proteins

1 reference

12 December 2020

Variational calculation of the normal modes of a large macromolecule: methods and some initial results

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.095927

Identifiers

DOI

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13 October 2017

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13 October 2017

PubMed publication ID

17483178

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