Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics (Q30486163)

18 August 2017

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

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principal component analysis

18 August 2017

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Ivet Bahar

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author name string

Lee-Wei Yang

series ordinal

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18 August 2017

Eran Eyal

series ordinal

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18 August 2017

Akio Kitao

series ordinal

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18 August 2017

language of work or name

English

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publication date

15 January 2009

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18 August 2017

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18 August 2017

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18 August 2017

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18 August 2017

606-614

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

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Relation between native ensembles and experimental structures of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Coarse-grained normal mode analysis in structural biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Conformational changes observed in enzyme crystal structures upon substrate binding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Simultaneous determination of protein structure and dynamics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Identifiying human MHC supertypes using bioinformatic methods.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Principal components analysis of protein structure ensembles calculated using NMR data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Anisotropy of fluctuation dynamics of proteins with an elastic network model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Essential dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

A comprehensive and non-redundant database of protein domain movements

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Dynamite: a simple way to gain insight into protein motions.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Using a neural network and spatial clustering to predict the location of active sites in enzymes

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Analysis of catalytic residues in enzyme active sites

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Effect of solvent on collective motions in globular protein.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2647834

Functional modes of proteins are among the most robust

26 November 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Free-energy landscape of kinesin by a realistic lattice model

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12 December 2020

Protein structural change upon ligand binding: linear response theory

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12 December 2020

Large-amplitude nonlinear motions in proteins

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12 December 2020

10.1093/BIOINFORMATICS/BTP023

Identifiers

DOI

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journals/bioinformatics/YangEBK09

18 August 2017

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DBLP Dataset 2021-01-02

28 January 2021

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18 August 2017

PubMed publication ID

19147661

1 reference