Iterative cluster-NMA: A tool for generating conformational transitions in proteins (Q30496342)

19 October 2017

Iterative cluster-NMA: A tool for generating conformational transitions in proteins (English)

1 reference

19 October 2017

Adam D Schuyler

1

1 reference

19 October 2017

Robert L Jernigan

2

1 reference

19 October 2017

Pradman K Qasba

3

1 reference

19 October 2017

Boopathy Ramakrishnan

4

1 reference

19 October 2017

Gregory S Chirikjian

5

1 reference

19 October 2017

language of work or name

English

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publication date

1 February 2009

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19 October 2017

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19 October 2017

74

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19 October 2017

3

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19 October 2017

760-776

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Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes

19 October 2017

1 reference

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Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach

14 July 2018

1 reference

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Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

14 July 2018

1 reference

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The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

14 July 2018

1 reference

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

14 July 2018

1 reference

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Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

14 July 2018

1 reference

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

14 July 2018

1 reference

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Conformational transitions of adenylate kinase: switching by cracking

14 July 2018

1 reference

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EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

14 July 2018

1 reference

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Analysis of domain movements in glutamine-binding protein with simple models

14 July 2018

1 reference

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

14 July 2018

1 reference

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A natural coarse graining for simulating large biomolecular motion

14 July 2018

1 reference

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

14 July 2018

1 reference

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Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

14 July 2018

1 reference

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A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure

14 July 2018

1 reference

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Can conformational change be described by only a few normal modes?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

A network representation of protein structures: implications for protein stability.

14 July 2018

1 reference

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Coarse-grained normal mode analysis in structural biology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA.

14 July 2018

1 reference

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Coarse-grained models for proteins

14 July 2018

1 reference

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Rigid-cluster models of conformational transitions in macromolecular machines and assemblies

14 July 2018

1 reference

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Protein unfolding: rigidity lost

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Single-molecule fluorescence resonance energy transfer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Conformational change of proteins arising from normal mode calculations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Anisotropy of fluctuation dynamics of proteins with an elastic network model

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Conformational changes studied by cryo-electron microscopy

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

14 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Identification of side-chain clusters in protein structures by a graph spectral method.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Crystal structures of the bovine beta 4galactosyltransferase catalytic domain and its complex with uridine diphosphogalactose

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Protein dynamics simulations from nanoseconds to microseconds

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Probing molecular motion by NMR.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

A simplified representation of protein conformations for rapid simulation of protein folding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

A Comparison Between Elastic Network Interpolation and MD Simulation of 16S Ribosomal RNA

14 July 2018

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Crossref

https://api.crossref.org/works/10.1002%2FPROT.22200

An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Protein conformational transitions explored by mixed elastic network models.

26 November 2018

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Interpreting correlated motions using normal mode analysis.

26 November 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930202

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=2930202

Normal mode analysis of proteins: a comparison of rigid cluster modes with C(alpha) coarse graining.

26 November 2018

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

26 November 2018

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

26 November 2018

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Protein flexibility and dynamics using constraint theory

26 November 2018

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12 December 2020

Normal mode analysis of G-actin

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12 December 2020

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

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12 December 2020

Elastic models of conformational transitions in macromolecules

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12 December 2020

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

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12 December 2020

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

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12 December 2020

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12 December 2020

Identifiers

DOI

10.1002/PROT.22200

1 reference

19 October 2017

1 reference

19 October 2017

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