Constraint counting on RNA structures: linking flexibility and function (Q37461649)

20 August 2017

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title

Constraint counting on RNA structures: linking flexibility and function (English)

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20 August 2017

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1

Simone Fulle

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20 August 2017

Holger Gohlke

2

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20 August 2017

4 May 2009

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20 August 2017

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20 August 2017

49

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20 August 2017

2

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20 August 2017

181-188

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RNA dynamics: it is about time.

20 August 2017

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Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA

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Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

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Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide

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Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps

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The relative flexibility of B-DNA and A-RNA duplexes: database analysis

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NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.

7 January 2021

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Molecular dynamics simulations of biomolecules

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Recent advances in the study of nucleic acid flexibility by molecular dynamics

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Molecular dynamics simulations of RNA: an in silico single molecule approach.

7 January 2021

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Global ribosome motions revealed with elastic network model

7 January 2021

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Exploring global motions and correlations in the ribosome

7 January 2021

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Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

7 January 2021

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

7 January 2021

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A ratchet-like inter-subunit reorganization of the ribosome during translocation

7 January 2021

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Multiscale modeling of nucleic acids: insights into DNA flexibility

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

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

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Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms

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Anisotropy of fluctuation dynamics of proteins with an elastic network model

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

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

7 January 2021

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Revealing unique properties of the ribosome using a network based analysis

7 January 2021

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Analyzing the flexibility of RNA structures by constraint counting

7 January 2021

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Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding

7 January 2021

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Protein flexibility predictions using graph theory

7 January 2021

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Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory.

7 January 2021

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Constrained geometric simulation of diffusive motion in proteins

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Protein unfolding: rigidity lost

7 January 2021

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A guide to ions and RNA structure

7 January 2021

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A natural coarse graining for simulating large biomolecular motion

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Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

7 January 2021

1 reference

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Resolving the motional modes that code for RNA adaptation

7 January 2021

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iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge

7 January 2021

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Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.

7 January 2021

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Identifying protein folding cores from the evolution of flexible regions during unfolding

7 January 2021

1 reference

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Size, shape, and flexibility of RNA structures

7 January 2021

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Water and ion binding around RNA and DNA (C,G) oligomers

7 January 2021

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Nucleic acid solvation: from outside to insight.

7 January 2021

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Molecular dynamics simulations of solvated yeast tRNA(Asp).

7 January 2021

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A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns

7 January 2021

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An optimized potential function for the calculation of nucleic acid interaction energies I. base stacking

7 January 2021

2 references

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7 January 2021

https://api.crossref.org/works/10.1016%2FJ.YMETH.2009.04.004

inferred from DOI database lookup

7 January 2021

based on heuristic

Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2009.04.004

The ribosomal exit tunnel functions as a discriminating gate

7 January 2021

1 reference

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Structural insight into the role of the ribosomal tunnel in cellular regulation

7 January 2021

1 reference

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Three-dimensional structures of translating ribosomes by Cryo-EM.

7 January 2021

1 reference

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Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins.

7 January 2021

1 reference

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7 January 2021

1 reference

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The structural basis of ribosome activity in peptide bond synthesis

7 January 2021

1 reference

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The Geometry of the Ribosomal Polypeptide Exit Tunnel

7 January 2021

1 reference

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The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

7 January 2021

1 reference

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The Structural Basis of Large Ribosomal Subunit Function

7 January 2021

1 reference

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Folding zones inside the ribosomal exit tunnel

7 January 2021

1 reference

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Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit

7 January 2021

1 reference

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Ribosomal antibiotics: structural basis for resistance, synergism and selectivity

7 January 2021

1 reference

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Ribosomal Crystallography: Initiation, Peptide Bond Formation, and Amino Acid Polymerization are Hampered by Antibiotics

7 January 2021

1 reference

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Chloramphenicol resistance mutations in the single 23S rRNA gene of the archaeon Halobacterium halobium

7 January 2021

1 reference

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The structures of four macrolide antibiotics bound to the large ribosomal subunit

7 January 2021

1 reference

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Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant

7 January 2021

1 reference

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Regulatory nascent peptides in the ribosomal tunnel

7 January 2021

1 reference

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Translation arrest requires two-way communication between a nascent polypeptide and the ribosome.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2009.04.004

Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements

7 January 2021

1 reference

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Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair

7 January 2021

1 reference

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Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study

7 January 2021

1 reference

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10.1016/J.YMETH.2009.04.004

7 January 2021

Identifiers

DOI

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20 August 2017

1 reference

PubMed ID

19398009