(Q35565495)

8 August 2017

Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change (English)

1 reference

8 August 2017

3

Douglas H Turner

1 reference

8 August 2017

Keith P Van Nostrand

1

1 reference

PubMed ID

22116780

8 August 2017

Scott D Kennedy

series ordinal

2

1 reference

PubMed ID

22116780

8 August 2017

David H Mathews

series ordinal

4

1 reference

8 August 2017

1 November 2011

1 reference

Journal of Chemical Theory and Computation

8 August 2017

1 reference

8 August 2017

7

1 reference

8 August 2017

11

1 reference

8 August 2017

3779-3792

1 reference

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies.

8 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Free energy profile of RNA hairpins: a molecular dynamics simulation study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

LOOS: an extensible platform for the structural analysis of simulations.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

RNA folding: thermodynamic and molecular descriptions of the roles of ions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Optimization by Simulated Annealing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

In silico design of small RNA switches.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Structures of RNA switches: insight into molecular recognition and tertiary structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

The Amber biomolecular simulation programs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Solution structure of an RNA internal loop with three consecutive sheared GA pairs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Geometric nomenclature and classification of RNA base pairs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Induced fit in RNA-protein recognition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Dynamics of translation on the ribosome: molecular mechanics of translocation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Adaptive recognition in RNA complexes with peptides and protein modules

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Classical electrostatics in biology and chemistry

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Incorporating variable dielectric environments into the generalized Born model

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3221466

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

26 September 2018

1 reference

12 December 2020

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

1 reference

12 December 2020

Analysis of global conformational transitions in ribozymes

1 reference

12 December 2020

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point

1 reference

12 December 2020

A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods

1 reference

12 December 2020

Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation

1 reference

12 December 2020

Convergence of molecular dynamics simulations of membrane proteins

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT200223Q

1 reference

8 August 2017

1 reference

8 August 2017

1 reference

PubMed ID

22116780