(Q37610797)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

review article

1 reference

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

author name string

Lee-Wei Yang

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

Choon-Peng Chng

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

language of work or name

1 reference

4 March 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

Bioinformatics and Biology Insights

9 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

volume

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

page(s)

25-45

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

Coarse-grained free energy functions for studying protein conformational changes: a double-well network model

9 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Deciphering protein dynamics from NMR data using explicit structure sampling and selection

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

High-throughput modeling and analysis of protein structural dynamics.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Protein structural variation in computational models and crystallographic data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Application of a Theory of Enzyme Specificity to Protein Synthesis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Reorientational contact-weighted elastic network model for the prediction of protein dynamics: comparison with NMR relaxation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Coarse-grained normal mode analysis in structural biology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Coarse-grained models for proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Simulation of F-actin filaments of several microns

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

The Xplor-NIH NMR molecular structure determination package

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Flexibility and packing in proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Anisotropy of fluctuation dynamics of proteins with an elastic network model

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Use of TLS parameters to model anisotropic displacements in macromolecular refinement

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Proteins with similar architecture exhibit similar large-scale dynamic behavior

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Folding funnels and binding mechanisms

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Investigating protein dynamics in collective coordinate space

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Dynamics of folded proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

An analysis of core deformations in protein superfamilies

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

vGNM: a better model for understanding the dynamics of proteins in crystals

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

oGNM: online computation of structural dynamics using the Gaussian Network Model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Conformational change of proteins arising from normal mode calculations

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Stability and dynamics of virus capsids described by coarse-grained modeling

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Anisotropic network model: systematic evaluation and a new web interface.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Maturation dynamics of bacteriophage HK97 capsid

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Global ribosome motions revealed with elastic network model

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Molecular mechanisms of chaperonin GroEL-GroES function

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Analysis of domain motions by approximate normal mode calculations.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

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

3 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735964

Analysis of domain motions in large proteins

3 December 2018

1 reference

12 December 2020

Collective variable description of small-amplitude conformational fluctuations in a globular protein

1 reference

12 December 2020

Allostery in a coarse-grained model of protein dynamics

1 reference

12 December 2020

Energy landscape of a native protein: jumping-among-minima model

1 reference

12 December 2020

Protein structural change upon ligand binding: linear response theory

1 reference

12 December 2020

Functional modes of proteins are among the most robust

1 reference

12 December 2020

Identifiers

DOI

10.4137/BBI.S460

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812764%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

PubMed publication ID

19812764

1 reference