(Q36002495)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

title

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

2

1 reference

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19 February 2020

Giovanni Bussi

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

author name string

Giovanni Pinamonti

series ordinal

1

1 reference

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19 February 2020

Cristian Micheletti

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

language of work or name

English

0 references

publication date

17 July 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

volume

43

1 reference

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19 February 2020

issue

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

page(s)

7260-7269

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

19 February 2020

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Elastic Network Models of Nucleic Acids Flexibility

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Computer Folding of RNA Tetraloops? Are We There Yet?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

The expanding view of RNA and DNA function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Elastic network models capture the motions apparent within ensembles of RNA structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

RNA secondary structure modeling at consistent high accuracy using differential SHAPE.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Hierarchy of RNA functional dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

RNA 3D structure prediction by using a coarse-grained model and experimental data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

The mechanisms of RNA SHAPE chemistry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Exploring RNA structural codes with SHAPE chemistry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Analyzing the flexibility of RNA structures by constraint counting

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Canonical sampling through velocity rescaling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Comparison of multiple Amber force fields and development of improved protein backbone parameters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Molecular dynamics simulations of sarcin-ricin rRNA motif.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Mechanical unfolding of RNA hairpins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Development and testing of a general amber force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Flexibility and packing in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Anisotropy of fluctuation dynamics of proteins with an elastic network model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Relationship between internucleotide linkage geometry and the stability of RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Ionic strength independence of charge distributions in solvation of biomolecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Physics-based de novo prediction of RNA 3D structures.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Comparison of tRNA motions in the free and ribosomal bound structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

The role of nucleobase interactions in RNA structure and dynamics.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Coarse-grained simulations of RNA and DNA duplexes

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Global ribosome motions revealed with elastic network model

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Quantitative analysis of nucleic acid three-dimensional structures.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

Analysis of domain motions by approximate normal mode calculations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551938

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

23 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

A solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

RNA Unwinding from Reweighted Pulling Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

The role of water in host-guest interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV708

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

21 January 2018

1 reference

12 December 2020

Allostery in a coarse-grained model of protein dynamics

1 reference

12 December 2020

A nucleotide-level coarse-grained model of RNA

1 reference

12 December 2020

Coarse-grained model for predicting RNA folding thermodynamics

1 reference

12 December 2020

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKV708

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

1 reference

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

PubMed publication ID

26187990

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26187990%20AND%20SRC:MED&resulttype=core&format=json