(Q35124317)

6 August 2017

title

Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings (English)

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6 August 2017

main subject

computational biology

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nearest neighbour algorithm

inferred from title

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1 reference

5

Brent M Znosko

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6 August 2017

Charles A Johnson

1

1 reference

6 August 2017

Richard J Bloomingdale

2

1 reference

6 August 2017

Vikram E Ponnusamy

3

1 reference

6 August 2017

Conor A Tillinghast

4

1 reference

6 August 2017

Michael Lewis

6

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6 August 2017

language of work or name

English

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publication date

30 June 2011

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Journal of Physical Chemistry B

6 August 2017

published in

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6 August 2017

volume

115

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6 August 2017

issue

29

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6 August 2017

page(s)

9244-9251

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Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?

6 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Classification and energetics of the base-phosphate interactions in RNA

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

The binding orientation of a norindenoisoquinoline in the topoisomerase I-DNA cleavage complex is primarily governed by pi-pi stacking interactions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Nature and magnitude of aromatic stacking of nucleic acid bases

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Stacking interactions and the twist of DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

An analysis of the different behavior of DNA and RNA through the study of the mutual relationship between stacking and hydrogen bonding

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

The post-SCF quantum chemistry characteristics of the guanine-guanine stacking B-DNA.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Nearest neighbor parameters for inosine x uridine pairs in RNA duplexes.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Role of solvation in the energy stabilization inside the hydrophobic core of the protein rubredoxin

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Comment on the Correct Use of Continuum Solvent Models

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Efficient Calculation of Many Stacking and Pairing Free Energies in DNA from a Few Molecular Dynamics Simulations

16 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3142330

Face-to-face arene-arene binding energies: dominated by dispersion but predicted by electrostatic and dispersion/polarizability substituent constants

16 November 2018

1 reference

12 December 2020

Assessment of the Performance of the M05−2X and M06−2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules

1 reference

12 December 2020

Characterizing the strength of individual hydrogen bonds in DNA base pairs

1 reference

12 December 2020

Stacking energies for average B-DNA structures from the combined density functional theory and symmetry-adapted perturbation theory approach

1 reference

12 December 2020

Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: NonempiricalAb InitioCalculations

1 reference

12 December 2020

Improved nearest-neighbor parameters for predicting DNA duplex stability

1 reference

12 December 2020

Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry

1 reference

12 December 2020

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

1 reference

12 December 2020

Interaction energy contributions of H-bonded and stacked structures of the AT and GC DNA base pairs from the combined density functional theory and intermolecular perturbation theory approach

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP2012733

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6 August 2017

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6 August 2017

1 reference