(Q34182722)

31 July 2017

title

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates (English)

1 reference

31 July 2017

0 references

Jaroslav Koca

6

0 references

Jirí Sponer

object named as

Jirí Sponer

7

0 references

Imre Berger

object named as

Imre Berger

5

0 references

Thomas E. Cheatham, III

2

object named as

Thomas E Cheatham

1 reference

31 July 2017

Richard Stefl

1

1 reference

31 July 2017

Nad'a Spacková

3

1 reference

31 July 2017

Eva Fadrná

4

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 September 2003

1 reference

31 July 2017

1 reference

31 July 2017

volume

85

1 reference

31 July 2017

issue

3

1 reference

31 July 2017

page(s)

1787-1804

1 reference

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

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Crystal structure of parallel quadruplexes from human telomeric DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

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=1303352

Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex 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=1303352

Cooperativity in drug-DNA recognition: a molecular dynamics study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Contribution of translational and rotational motions to molecular association in aqueous solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Targeting telomeres and telomerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Telomere maintenance mechanisms as a target for drug 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=1303352

Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC).

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Interaction of human DNA topoisomerase I with G-quartet structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Molecular dynamics simulation 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=1303352

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=1303352

G-quadruplex DNA: a potential target for anti-cancer drug design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

G-quadruplexes as targets for drug design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Structure-activity relationships among guanine-quadruplex telomerase inhibitors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

An A-type double helix of DNA having B-type puckering of the deoxyribose rings.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The development of telomerase inhibitors: the G-quartet approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Multistranded DNA structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Solution structure of a Na cation stabilized DNA quadruplex containing G.G.G.G and G.C.G.C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald molecular dynamics 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=1303352

Structural equilibrium of DNA represented with different force fields

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

DNA tetraplex formation in the control region of c-myc

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: thermodynamic evidence for three linked association pathways

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The statistical-thermodynamic basis for computation of binding affinities: a critical review

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Reduced surface: an efficient way to compute molecular surfaces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

MOLMOL: a program for display and analysis of macromolecular structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The beta subunit of Oxytricha telomere-binding protein promotes G-quartet formation by telomeric DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The high-resolution crystal structure of a parallel-stranded guanine tetraplex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Salt effects on ligand-DNA binding. Minor groove binding antibiotics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The fragile X syndrome single strand d(CGG)n nucleotide repeats readily fold back to form unimolecular hairpin structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Electrostatic interactions in macromolecules: theory and applications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Quadruplex structure of Oxytricha telomeric DNA oligonucleotides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Contributions to the binding free energy of ligands to avidin and streptavidin.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The electrostatic contribution to the B to Z transition of DNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Strand orientation in the DNA quadruplex formed from the Oxytricha telomere repeat oligonucleotide d(G4T4G4) in solution.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303352

Optimised parameters for A-DNA and B-DNA

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Collective motion artifacts arising in long-duration molecular dynamics simulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

A nanosecond molecular dynamics study of antiparallel d(G)7 quadruplex structures: effect of the coordinated cations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Theoretical Studies of d(A:T)-Based Parallel-Stranded DNA Duplexes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

The human insulin gene-linked polymorphic region adopts a G-quartet structure in chromatin assembled in vitro

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Accelerated assembly of G-quadruplex structures by a small molecule

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Selective interactions of cationic porphyrins with G-quadruplex structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Ligand binding affinity prediction by linear interaction energy methods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Free Energy of Ionic Hydration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Synthetic Adenine Receptors: Direct Calculation of Binding Affinity and Entropy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Molecular modeling studies on G-quadruplex complexes of telomerase inhibitors: structure-activity relationships

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Nanosecond Molecular Dynamics of Zipper-like DNA Duplex Structures Containing Sheared G·A Mismatch Pairs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

7 January 2021

Nonplanar DNA Base Pairs

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

G.C base pair in parallel-stranded DNA--a novel type of base pairing: an ab initio quantum chemical study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

Effects of cationic porphyrins as G-quadruplex interactive agents in human tumor cells

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12944293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Porphyrins can catalyze the interconversion of DNA quadruplex structural types

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12944293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A smooth particle mesh Ewald method

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974608-6

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(03)74608-6

1 reference

31 July 2017

1 reference

31 July 2017

1 reference