(Q33848442)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

23 December 2019

title

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

23 December 2019

0 references

0 references

1 reference

3

1 reference

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23 December 2019

4

Darrin M York

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

23 December 2019

author name string

Evelyn Mayaan

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

23 December 2019

Adam Moser

series ordinal

2

1 reference

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23 December 2019

publication date

1 January 2007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computational Chemistry

23 December 2019

published in

1 reference

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23 December 2019

volume

28

1 reference

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23 December 2019

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

23 December 2019

page(s)

495-507

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

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

23 December 2019

cites work

1 reference

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Empirical force fields for biological macromolecules: overview and issues.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Transition state stabilization by a catalytic RNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Simulations of nucleic acids and their complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Catalytic strategies of the hepatitis delta virus ribozymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

siRNA-directed inhibition of HIV-1 infection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Profiling alternative splicing on fiber-optic arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Development and current status of the CHARMM force field for nucleic acids.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Toward antisense oligonucleotide therapy for cancer: ISIS compounds in clinical development.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Ribozyme structures and mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Nucleic acids: theory and computer simulation, Y2K.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Relationship between internucleotide linkage geometry and the stability of RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Nucleic acid molecular switches

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

A re-investigation of the thio effect at the hammerhead cleavage site

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Crystal structure of a hepatitis delta virus ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Ion-RNA interactions in the RNA pseudoknot of a ribosomal frameshifting site: molecular modeling studies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Simulations of the molecular dynamics of nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

The structural basis of hammerhead ribozyme self-cleavage

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

The intervening sequence RNA of Tetrahymena is an enzyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Ribonuclease P: an enzyme with an essential RNA component

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Localization of transcribed regions on extrachromosomal ribosomal RNA genes of Tetrahymena thermophila by R-loop mapping

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Crystals of a hammerhead ribozyme.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2869295

Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

29 October 2018

1 reference

12 December 2020

Explanation by a putative triester-like mechanism for the thio effects and Mn2+ rescues in reactions catalyzed by a hammerhead ribozyme

1 reference

12 December 2020

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

1 reference

12 December 2020

Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

1 reference

12 December 2020

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

1 reference

12 December 2020

Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases

1 reference

12 December 2020

Catalytic role of metal ion in the selection of competing reaction paths: a first principles molecular dynamics study of the enzymatic reaction in ribozyme

1 reference

12 December 2020

Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

1 reference

12 December 2020

Detection of a proton-transfer process by kinetic solvent isotope effects in NH(4)(+)-mediated reactions catalyzed by a hammerhead ribozyme

1 reference

12 December 2020

NMR-based reappraisal of the coordination of a metal ion at the pro-Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme

1 reference

12 December 2020

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

1 reference

12 December 2020

Molecular dynamics investigations of hammerhead ribozyme RNA

1 reference

12 December 2020

Activities and relative affinities of divalent metals in unmodified and phosphorothioate-substituted hammerhead ribozymes

1 reference

12 December 2020

1 reference

12 December 2020

The internal equilibrium of the hammerhead ribozyme reaction

1 reference

12 December 2020

Comparison of metal-ion-dependent cleavages of RNA by a DNA enzyme and a hammerhead ribozyme

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.20474

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

23 December 2019

DBLP publication ID

journals/jcc/MayaanMMY07

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17186477%20AND%20SRC:MED&resulttype=core&format=json

23 December 2019

PubMed publication ID

17186477

1 reference