Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes (Q42348373)

27 October 2017

Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes (English)

1 reference

27 October 2017

H Vashisth

1 reference

PMC publication ID

3505029

27 October 2017

C L Brooks

series ordinal

1 reference

27 October 2017

1 November 2012

1 reference

Journal of Physical Chemistry Letters

27 October 2017

1 reference

27 October 2017

1 reference

27 October 2017

1 reference

27 October 2017

3379-3384

1 reference

"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.

27 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Large conformational changes in proteins: signaling and other functions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Coarse-grained normal mode analysis in structural biology

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Escaping free-energy minima

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Conformational change of proteins arising from normal mode calculations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Collective protein dynamics in relation to function

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Collective variable description of native protein dynamics

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Single-sweep methods for free energy calculations

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505029

Some recent techniques for free energy calculations

1 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23185650

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23185650

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JZ301650Q

1 reference

27 October 2017

1 reference

PMC publication ID

3505029

27 October 2017

PubMed publication ID

23185650

1 reference

PMC publication ID

3505029