Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study (Q36668899)

15 August 2017

Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study (English)

1 reference

15 August 2017

Mahmoud Moradi

1

1 reference

15 August 2017

Volodymyr Babin

series ordinal

2

1 reference

15 August 2017

Christopher Roland

series ordinal

3

1 reference

15 August 2017

Celeste Sagui

series ordinal

4

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15 August 2017

language of work or name

English

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publication date

26 October 2012

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15 August 2017

Nucleic Acids Research

1 reference

15 August 2017

41

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15 August 2017

1

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15 August 2017

33-43

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Creative Commons Attribution-NonCommercial 3.0 Unported

15 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Crystal structure of a junction between two Z-DNA helices

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Two distinct overstretched DNA states.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Conformations and free energy landscapes of polyproline peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Molecular mechanisms for the B-Z transition in the example of poly[d(G-C) x d(G-C)] polymers. A critical review

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Z-DNA-forming sequences generate large-scale deletions in mammalian cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

The Amber biomolecular simulation programs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

The stretched intermediate model of B-Z DNA transition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Exploring protein native states and large-scale conformational changes with a modified generalized born model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

DNA helix: the importance of being GC-rich

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Z-DNA-binding proteins can act as potent effectors of gene expression in vivo

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Escaping free-energy minima

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Long time dynamics of complex systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Left-handed Z-DNA: structure and function

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Local elevation: a method for improving the searching properties of molecular dynamics simulation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

DNA structural dynamics: longitudinal breathing as a possible mechanism for the B in equilibrium Z transition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

The chemistry and biology of left-handed Z-DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Locations of Z-DNA in polytene chromosomes.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Evidence for a new Z-type left-handed DNA helix: properties of Z(WC)-DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Molecular structure of a left-handed double helical DNA fragment at atomic resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

30 September 2017

Left-handed DNA in vivo.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Raison d'être and structural model for the B-Z transition of poly d(G-C).poly d(G-C).

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

PPII propensity of multiple-guest amino acids in a proline-rich environment

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Adaptively biased molecular dynamics for free energy calculations

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Computation of free energy profiles with parallel adaptive dynamics.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

DNA: an extensible molecule.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Left-handed Z-DNA binding by the recA protein of Escherichia coli.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3592462

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

20 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1003

Calculating relative transition rates with driven nonequilibrium simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1003

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1003

Nonequilibrium Equality for Free Energy Differences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1003

Equilibrium Free Energies from Nonequilibrium Metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1003

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

21 January 2018

1 reference

12 December 2020

Applying the stochastic difference equation to DNA conformational transitions: a study of B-Z and B-A DNA transitions

1 reference

12 December 2020

Characterization of intermediate conformational states in the B in equilibrium Z transitions of poly(dG-dC).poly(dG-dC)

1 reference

12 December 2020

Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus

1 reference

12 December 2020

A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties

1 reference

12 December 2020

Left-handed DNA and the synaptic pairing reaction promoted by Ustilago rec1 protein

1 reference

12 December 2020

Overstretching and force-driven strand separation of double-helix DNA

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKS1003

1 reference

15 August 2017

1 reference

15 August 2017

PubMed publication ID

23104380

1 reference