Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs (Q33595570)

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English	Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs	scientific article

Statements

scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs (English)

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

object named as

Jiri Sponer

3

0 references

Douglas H. Turner

5

object named as

Douglas H Turner

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

author name string

Ilyas Yildirim

1

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Harry A Stern

2

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Nada Spackova

4

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

publication date

2 July 2009

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Journal of Chemical Theory and Computation

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

5

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

8

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

2088-2100

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

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Nature and magnitude of aromatic stacking of nucleic acid bases

1 reference

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Nucleic acid solvation: from outside to insight.

1 reference

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Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs †

1 reference

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21 June 2018

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

1 reference

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21 June 2018

RNA challenges for computational chemists

1 reference

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Exploring global motions and correlations in the ribosome

1 reference

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Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

1 reference

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Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

1 reference

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Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis

1 reference

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Rapid compaction during RNA folding

1 reference

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1 reference

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1 reference

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Geometric nomenclature and classification of RNA base pairs

1 reference

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Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

1 reference

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21 June 2018

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2807739

21 June 2018

Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach

1 reference

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A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993

1 reference

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21 June 2018

Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics

1 reference

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The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser)

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GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain

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A major family of motifs involving G.A mismatches in ribosomal RNA.

1 reference

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Three-dimensional structure of a hammerhead ribozyme

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Comparative anatomy of 16-S-like ribosomal RNA.

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Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

1 reference

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1 reference

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1 reference

https://pubmed.ncbi.nlm.nih.gov/20090924

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

1 reference

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1 reference

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Identifiers

10.1021/CT800540C

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

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