(Q36422866)

English

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. (English)

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

0 references

0 references

4

object named as

Michal Otyepka

0 references

object named as

Miroslav Krepl

1

0 references

5

object named as

Pavel Banáš

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

Thomas E. Cheatham, III

7

object named as

Thomas E Cheatham

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

6

object named as

Jaroslav Koča

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

author name string

Marie Zgarbová

2

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

Petr Stadlbauer

3

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

Petr Jurečka

8

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

Jiří Sponer

9

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

publication date

5 June 2012

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

Journal of Chemical Theory and Computation

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

8

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

7

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

2506-2520

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Evaluation of DNA Force Fields in Implicit Solvation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Fluorine in medicinal chemistry: β-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

DNA conformations and their sequence preferences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Molecular dynamics simulations and their application to four-stranded DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Molecular dynamics simulations of sarcin-ricin rRNA motif.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Crystal structure of the potassium form of an Oxytricha nova G-quadruplex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

X-ray analysis of an RNA tetraplex (UGGGGU)4 with divalent Sr2+ ions at subatomic resolution (0.61 A)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

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=3506181

30 September 2017

"...the tyranny of the lattice...".

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

The molecular structure of the left-handed Z-DNA double helix at 1.0-A atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

30 September 2017

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

28 June 2018

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

28 June 2018

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

21 September 2018

Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

21 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

21 September 2018

Dependence of A-RNA simulations on the choice of the force field and salt strength

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506181

4 December 2018

Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex

1 reference

https://pubmed.ncbi.nlm.nih.gov/23197943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/23197943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Left-handed double helical DNA: variations in the backbone conformation

1 reference

https://pubmed.ncbi.nlm.nih.gov/23197943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Theoretical Analysis of the Base Stacking in DNA: Choice of the Force Field and a Comparison with the Oligonucleotide Crystal Structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/23197943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

1 reference

https://pubmed.ncbi.nlm.nih.gov/23197943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/CT300275S

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q36422866&oldid=1518756191"