(Q34694568)

4 August 2017

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title

Coarse-grained normal mode analysis in structural biology (English)

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4 August 2017

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1

Ivet Bahar

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author name string

A J Rader

series ordinal

2

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4 August 2017

publication date

1 October 2005

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Current Opinion in Structural Biology

4 August 2017

published in

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4 August 2017

volume

15

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4 August 2017

issue

5

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4 August 2017

page(s)

586-592

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Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies

4 August 2017

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Normal-modes-based prediction of protein conformational changes guided by distance constraints

7 July 2018

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7 July 2018

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An analysis of core deformations in protein superfamilies

7 July 2018

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Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase

7 July 2018

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Dynamical transition and proteinquake in photoactive yellow protein

7 July 2018

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Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

7 July 2018

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Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data

7 July 2018

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Mining frequent patterns in protein structures: a study of protease families.

7 July 2018

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ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

7 July 2018

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Molecular mechanism of domain swapping in proteins: an analysis of slower motions

7 July 2018

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Identification of core amino acids stabilizing rhodopsin

7 July 2018

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On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models

7 July 2018

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ProMode: a database of normal mode analyses on protein molecules with a full-atom model.

7 July 2018

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

7 July 2018

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Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

7 July 2018

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Molecular dynamics simulations of peptides and proteins with amplified collective motions

7 July 2018

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MolMovDB: analysis and visualization of conformational change and structural flexibility

7 July 2018

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

7 July 2018

1 reference

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

7 July 2018

1 reference

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Efficient generation of feasible pathways for protein conformational transitions

7 July 2018

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Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

7 July 2018

1 reference

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Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

7 July 2018

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

7 July 2018

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How to describe protein motion without amino acid sequence and atomic coordinates.

7 July 2018

1 reference

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Dynamics of large proteins through hierarchical levels of coarse-grained structures.

7 July 2018

1 reference

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

7 July 2018

1 reference

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Conformational change of proteins arising from normal mode calculations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Anisotropy of fluctuation dynamics of proteins with an elastic network model

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Investigating protein dynamics in collective coordinate space

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Simple energy landscape model for the kinetics of functional transitions in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Domain motions and the open-to-closed conformational transition of an enzyme: a normal mode analysis of S-adenosyl-L-homocysteine hydrolase

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Maturation dynamics of bacteriophage HK97 capsid

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Automatic domain decomposition of proteins by a Gaussian Network Model.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Global ribosome motions revealed with elastic network model

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Predictions of protein flexibility: first-order measures

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Myosin flexibility: structural domains and collective vibrations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Analysis of domain motions by approximate normal mode calculations

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1482533

Molecular mastication mechanics

9 December 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Elastic Properties of Proteins: Insight on the Folding Process and Evolutionary Selection of Native Structures

1 reference

12 December 2020

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis

1 reference

12 December 2020

The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function

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12 December 2020

10.1016/J.SBI.2005.08.007

Identifiers

DOI

1 reference

4 August 2017

1 reference

4 August 2017

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