(Q34771947)

4 August 2017

title

Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models (English)

1 reference

4 August 2017

Lee-Wei Yang

1

1 reference

4 August 2017

language of work or name

English

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publication date

1 April 2011

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4 August 2017

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4 August 2017

volume

100

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4 August 2017

issue

7

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4 August 2017

page(s)

1784-1793

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Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives

4 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Protein elastic network models and the ranges of cooperativity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Application of elastic network models to proteins in the crystalline state

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

oGNM: online computation of structural dynamics using the Gaussian 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=3072623

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

An elastic network model of HK97 capsid maturation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

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=3072623

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=3072623

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

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=3072623

Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Structural flexibility in proteins: impact of the crystal environment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3072623

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=3072623

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=3072623

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=3072623

Vibrational normal-mode spectrum of globular proteins

9 December 2018

1 reference

12 December 2020

Comment on elastic network models and proteins

1 reference

12 December 2020

Functional modes of proteins are among the most robust

1 reference

12 December 2020

Allostery in a coarse-grained model of protein dynamics

1 reference

12 December 2020

10.1016/J.BPJ.2011.02.033

Identifiers

DOI

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4 August 2017

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4 August 2017

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