(Q41952799)

14 October 2017

Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions (English)

1 reference

14 October 2017

0 references

5

Douglas H Turner

1 reference

14 October 2017

3

Jason D Tubbs

1 reference

14 October 2017

Ilyas Yildirim

1

1 reference

14 October 2017

Harry A Stern

series ordinal

2

1 reference

14 October 2017

Scott D Kennedy

series ordinal

4

1 reference

14 October 2017

language of work or name

English

0 references

publication date

1 July 2011

1 reference

Journal of Physical Chemistry B

14 October 2017

1 reference

14 October 2017

115

1 reference

14 October 2017

29

1 reference

14 October 2017

9261-9270

1 reference

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Atomic accuracy in predicting and designing noncanonical RNA structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Architecture and secondary structure of an entire HIV-1 RNA genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Long-timescale molecular dynamics simulations of protein structure and function.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

RNA challenges for computational chemists

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern †

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Simulation and modeling of nucleic acid structure, dynamics and interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

RNA conformational classes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Theoretical methods for the simulation of nucleic acids.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Simulations of nucleic acids and their complexes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Molecular biology. Glimpses of a tiny RNA world

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Nucleic acids: theory and computer simulation, Y2K.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

The sarcin/ricin loop, a modular RNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Role of RNA in enzymatic activity of the reverse transcriptase of hepatitis B viruses.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

A quantitative model of the Escherichia coli 16 S RNA in the 30 S ribosomal subunit.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid)

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

RNA structure and NMR spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Laser temperature-jump study of stacking in adenylic acid polymers

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Force field parameters for rotation around chi torsion axis in nucleic acids

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3140773

Theory and applications of the generalized Born solvation model in macromolecular simulations

18 August 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Exploring the Essential Dynamics of B-DNA

1 reference

12 December 2020

Conformational Analysis of the Single-Stranded Ribonucleic Acid A-A-C-C. A One-Dimensional and Two-Dimensional Proton NMR Study at 500 MHz

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

The dynamics of nucleic-acid single-strand conformation changes. Oligo- and polyriboadenylic acids

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP2016006

1 reference

14 October 2017

1 reference

14 October 2017

PubMed publication ID

21721539

1 reference