Toward a consensus view of duplex RNA flexibility (Q34134724)

31 July 2017

Toward a consensus view of duplex RNA flexibility (English)

1 reference

31 July 2017

3

Modesto Orozco

1 reference

31 July 2017

Ignacio Faustino

1

1 reference

PubMed ID

20858433

31 July 2017

Alberto Pérez

series ordinal

2

1 reference

PubMed ID

20858433

31 July 2017

language of work or name

English

0 references

publication date

1 September 2010

1 reference

31 July 2017

1 reference

31 July 2017

99

1 reference

31 July 2017

6

1 reference

31 July 2017

1876-1885

1 reference

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Conformational analysis of nucleic acids revisited: Curves+

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

CHARMM: the biomolecular simulation program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Local and global effects of strong DNA bending induced during molecular dynamics simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

A short guide for molecular dynamics simulations of RNA systems.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Towards a molecular dynamics consensus view of B-DNA flexibility

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Determining promoter location based on DNA structure first-principles calculations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

A consensus view of protein dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Scalable molecular dynamics with NAMD

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Theoretical methods for the simulation of nucleic acids.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Functional siRNAs and miRNAs Exhibit Strand Bias

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Development and current status of the CHARMM force field for nucleic acids.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

A standard reference frame for the description of nucleic acid base-pair geometry.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Imino proton exchange and base-pair kinetics in RNA duplexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Representation of the secondary and tertiary structure of group I introns

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

RNA evolution and the origins of life

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Biological catalysis by RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

An unstable intermediate carrying information from genes to ribosomes for protein synthesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

DNAlive: a tool for the physical analysis of DNA at the genomic scale.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Dynamics of B-DNA on the microsecond time scale.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Kinking occurs during molecular dynamics simulations of small DNA minicircles.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Sequence-dependent elastic properties of DNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

The Nucleic Acid Database: A resource for nucleic acid science

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941024

Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature

28 October 2018

1 reference

12 December 2020

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

12 December 2020

Theoretical Analysis of Antisense Duplexes: Determinants of the RNase H Susceptibility

1 reference

12 December 2020

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

1 reference

12 December 2020

Comparison of molecular dynamics and harmonic mode calculations on RNA

1 reference

12 December 2020

The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA

1 reference

12 December 2020

An atomistic view to the gas phase proteome

1 reference

12 December 2020

Persistence length of RNA

1 reference

12 December 2020

Structure, Recognition Properties, and Flexibility of the DNA·RNA Hybrid

1 reference

12 December 2020

Exploring the Essential Dynamics of B-DNA

1 reference

12 December 2020

NAMD: a Parallel, Object-Oriented Molecular Dynamics Program

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1177/109434209601000401

10.1016/J.BPJ.2010.06.061

22 October 2022

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

20858433