Analyzing the flexibility of RNA structures by constraint counting (Q40799435)

23 September 2017

Analyzing the flexibility of RNA structures by constraint counting (English)

1 reference

23 September 2017

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1

Simone Fulle

1 reference

23 September 2017

Holger Gohlke

2

1 reference

PMCID

2480660

23 September 2017

language of work or name

English

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publication date

15 February 2008

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23 September 2017

1 reference

23 September 2017

94

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23 September 2017

11

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23 September 2017

4202-4219

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

23 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

A New Method for Coarse-Grained Elastic Normal-Mode Analysis

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

A natural coarse graining for simulating large biomolecular motion

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Simulating movement of tRNA into the ribosome during decoding

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

The Amber biomolecular simulation programs

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Drugs targeting the ribosome

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Single-molecule measurements of the persistence length of double-stranded RNA

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Origin of the intrinsic rigidity of DNA.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Gene regulation by riboswitches

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structure of HCV IRES domain II determined by NMR

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Implications of protein flexibility for drug discovery

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

The solution structure of the loop E region of the 5S rRNA from spinach chloroplasts

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Molecular dynamics simulations of biomolecules

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Protein unfolding: rigidity lost

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Steered molecular dynamics investigations of protein function.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Strategies for the Design of Drugs Targeting RNA and RNA-Protein Complexes

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Targeting RNA with small molecules

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Stitching together RNA tertiary architectures

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structure of the phylogenetically most conserved domain of SRP RNA.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Molecular dynamics simulations of solvated yeast tRNA(Asp).

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

The structural basis of hammerhead ribozyme self-cleavage

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

A network of heterogeneous hydrogen bonds in GNRA tetraloops

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Dynamics of transfer RNAs analyzed by normal mode calculation

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structure of the P1 helix from group I self-splicing introns

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Exceptionally stable nucleic acid hairpins

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structure of yeast phenylalanine tRNA at 3 Å resolution

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Anticodon-anticodon interaction induces conformational changes in tRNA: yeast tRNAAsp, a model for tRNA-mRNA recognition

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

A thermodynamic study of unusually stable RNA and DNA hairpins

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Detection of a major conformational change in transfer ribonucleic acid by laser light scattering

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

A crystallographic study of metal-binding to yeast phenylalanine transfer RNA

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structure of stem-loop IV of Tetrahymena telomerase RNA.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

A twisted tRNA intermediate sets the threshold for decoding

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

RNA as a drug target: chemical, modelling, and evolutionary tools

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Automated design of the surface positions of protein helices

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Assignment of the magnetic resonances of the imino protons and methyl protons of Bombyx mori tRNA(GlyGCC) and the effect of ion binding on its structure

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Size, shape, and flexibility of RNA structures

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Constrained geometric simulation of diffusive motion in proteins

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by MNMR 13C relaxation.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

13C NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Global ribosome motions revealed with elastic network model

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Sampling protein conformations and pathways

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Cross correlations between 13C-1H dipolar interactions and 15N chemical shift anisotropy in nucleic acids

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Protein flexibility predictions using graph theory

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Prediction of protein conformational freedom from distance constraints

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480660

Generic rigidity percolation: The pebble game

4 November 2018

1 reference

12 December 2020

Protein flexibility and dynamics using constraint theory

1 reference

12 December 2020

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

1 reference

12 December 2020

Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations

1 reference

12 December 2020

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

1 reference

12 December 2020

Structure of the RNA signal essential for translational frameshifting in HIV-1

1 reference

12 December 2020

Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element

1 reference

12 December 2020

Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

1 reference

12 December 2020

Counting out to the flexibility of molecules

1 reference

12 December 2020

What NMR Relaxation Can Tell Us about the Internal Motion of an RNA Hairpin: A Molecular Dynamics Simulation Study

1 reference

12 December 2020

Persistence length of RNA

1 reference

12 December 2020

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

1 reference

12 December 2020

Variations on a theme by Debye and Waller: from simple crystals to proteins

1 reference

12 December 2020

Rules governing the orientation of the 2'-hydroxyl group in RNA

1 reference

12 December 2020

Glass-forming tendency, percolation of rigidity, and onefold-coordinated atoms in covalent networks

1 reference

12 December 2020

10.1529/BIOPHYSJ.107.113415

Identifiers

DOI

1 reference

23 September 2017

1 reference

23 September 2017

1 reference

PMCID

2480660