(Q30589123)

25 June 2017

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title

Nucleic acids: theory and computer simulation, Y2K. (English)

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25 June 2017

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D L Beveridge

1

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25 June 2017

K J McConnell

series ordinal

2

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25 June 2017

publication date

1 April 2000

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Current Opinion in Structural Biology

25 June 2017

published in

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25 June 2017

volume

10

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25 June 2017

issue

2

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25 June 2017

page(s)

182-196

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Simulations of the molecular dynamics of nucleic acids

25 June 2017

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7 January 2021

Resolving the discrepancies among nucleic acid conformational analyses

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7 January 2021

Crystal structure analysis of a complete turn of B-DNA

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The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

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Influence of packing interactions on the average conformation of B-DNA in crystalline structures

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7 January 2021

Crystal studies of B-DNA: the answers and the questions

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7 January 2021

Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA.

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7 January 2021

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

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

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7 January 2021

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

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7 January 2021

The effects of truncating long-range forces on protein dynamics.

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7 January 2021

Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results

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7 January 2021

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

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7 January 2021

A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions

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7 January 2021

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

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7 January 2021

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

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7 January 2021

Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration

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7 January 2021

An all atom force field for simulations of proteins and nucleic acids

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7 January 2021

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

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7 January 2021

Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR.

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7 January 2021

Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method

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7 January 2021

Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations

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7 January 2021

Structural equilibrium of DNA represented with different force fields

1 reference

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7 January 2021

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation.

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7 January 2021

The GROMOS Biomolecular Simulation Program Package

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7 January 2021

Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator

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7 January 2021

Parametrization of aliphatic CHn united atoms of GROMOS96 force field

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7 January 2021

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

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7 January 2021

Semianalytical treatment of solvation for molecular mechanics and dynamics

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7 January 2021

Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model

1 reference

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7 January 2021

Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.

1 reference

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7 January 2021

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

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7 January 2021

Ionic effects beyond Poisson-Boltzmann theory

1 reference

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7 January 2021

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

1 reference

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7 January 2021

Curved DNA: design, synthesis, and circularization

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Estimation of wedge components in curved DNA.

1 reference

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7 January 2021

DNA bending at adenine . thymine tracts

1 reference

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7 January 2021

Bending and curvature calculations in B-DNA.

1 reference

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7 January 2021

Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains

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7 January 2021

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

1 reference

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7 January 2021

X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature

1 reference

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7 January 2021

Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG)

1 reference

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7 January 2021

Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA.

1 reference

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7 January 2021

The structure of an oligo(dA).oligo(dT) tract and its biological implications

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7 January 2021

TIT for TAT: the properties of inosine and adenosine in TATA box DNA.

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7 January 2021

Temperature-dependent ultraviolet resonance Raman spectroscopy of the premelting state of dA.dT DNA.

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7 January 2021

C-H.O hydrogen bonds in minor groove of A-tracts in DNA double helices.

1 reference

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7 January 2021

Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study

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7 January 2021

Conformational properties of the TATA-box binding sequence of DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Sequence-dependent dynamics of TATA-Box binding sites

1 reference

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7 January 2021

Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein

1 reference

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7 January 2021

Protein hydration density: theory, simulations and crystallography

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Hydration of the phosphate group in double-helical DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Hydration of the DNA bases is local

1 reference

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7 January 2021

Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies

1 reference

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7 January 2021

Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study

1 reference

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7 January 2021

Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation

1 reference

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7 January 2021

Observation of Spontaneous Base Pair Breathing Events in the Molecular Dynamics Simulation of a Difluorotoluene-Containing DNA Oligonucleotide

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Characterization of the minor groove environment in a drug-DNA complex: bisbenzimide bound to the poly[d(AT)].poly[d(AT)]duplex

1 reference

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7 January 2021

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

RNA hydration: a detailed look

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Salt effects on nucleic acids

1 reference

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7 January 2021

Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA.

1 reference

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7 January 2021

Molecular dynamics simulations of DNA in solutions with different counter-ions.

1 reference

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7 January 2021

Sodium and chlorine ions as part of the DNA solvation shell

1 reference

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7 January 2021

The molecular electrostatic potential, steric accessibility and hydration of Dickerson's B-DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG)

1 reference

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7 January 2021

Double helix at atomic resolution

1 reference

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7 January 2021

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending

1 reference

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7 January 2021

Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations

1 reference

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7 January 2021

A “Hydrat-Ion” Spine in a B-DNA Minor Groove

1 reference

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7 January 2021

DNA structure: cations in charge?

1 reference

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7 January 2021

DNA bending by asymmetric phosphate neutralization

1 reference

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7 January 2021

Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G

1 reference

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7 January 2021

DNA bending by small, mobile multivalent cations

1 reference

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7 January 2021

Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.

1 reference

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7 January 2021

Sequence-directed curvature of DNA

1 reference

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7 January 2021

Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2-C5) and d(G5-(GT4A4C)2-C5): effects of sequence polarity on DNA curvature

1 reference

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7 January 2021

Structural details of an adenine tract that does not cause DNA to bend

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Role of sugar re-puckering in the transition of A and B forms of DNA in solution. A molecular dynamics study

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7 January 2021

Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases

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7 January 2021

DNA conformation and dynamics

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7 January 2021

Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation

1 reference

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7 January 2021

Molecular dynamics simulations of solvated yeast tRNA(Asp).

1 reference

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7 January 2021

Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Wild-Type RNA MicrohelixAlaand 3:70 Variants: Molecular Dynamics Analysis of Local Helical Structure and Tightly Bound Water

1 reference

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7 January 2021

Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Continuum solvent studies of the stability of RNA hairpin loops and helices

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

The incompatibility of Popper's philosophy of science with genetics and molecular biology.

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7 January 2021

Progress in protein structure prediction: assessment of CASP3.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900076-2

7 January 2021

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

1 reference

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7 January 2021

10.1016/S0959-440X(00)00076-2

Identifiers

DOI

1 reference

25 June 2017

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