Parmbsc1: a refined force field for DNA simulations (Q36428161)

14 August 2017

Parmbsc1: a refined force field for DNA simulations (English)

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14 August 2017

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18

David A Case

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Alexandra Balaceanu

Alexandra Balaceanu

10

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Federica Battistini

Federica Battistini

12

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Pablo D. Dans

Pablo D Dans

2

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Agnes Noy

Agnes Noy

3

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Ignacio Faustino

Ignacio Faustino

5

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Guillem Portella

Guillem Portella

11

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Josep Lluís Gelpí

Josep Lluis Gelpí

13

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Carlos González

Carlos González

14

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Michele Vendruscolo

15

Michele Vendruscolo

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14 August 2017

17

Sarah A Harris

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14 August 2017

Alberto Pérez

4

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Modesto Orozco

19

Modesto Orozco

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14 August 2017

Ivan Ivani

1

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14 August 2017

Adam Hospital

6

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14 August 2017

Jürgen Walther

7

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14 August 2017

Pau Andrio

8

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14 August 2017

Ramon Goñi

9

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14 August 2017

Charles A Laughton

16

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14 August 2017

David A Case

18

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14 August 2017

16 November 2015

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full work available at URL

14 August 2017

http://eprints.whiterose.ac.uk/100211/

content deliverer

White Rose Research Online

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published in

Nature Methods

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14 August 2017

13

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1

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14 August 2017

55-58

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https://scigraph.springernature.com/pub.10.1038/nmeth.3658

14 August 2017

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

30 September 2017

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Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the "Gold Standard," CCSD(T) at the Complete Basis Set Limit?

30 September 2017

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Direct measurement of the dielectric polarization properties of DNA.

30 September 2017

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High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

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Dramatic effect of furanose C2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom

30 September 2017

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

30 September 2017

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30 September 2017

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A measure of bending in nucleic acids structures applied to A-tract DNA.

30 September 2017

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A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

30 September 2017

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Conformational analysis of nucleic acids revisited: Curves+

30 September 2017

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Towards a molecular dynamics consensus view of B-DNA flexibility

30 September 2017

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Kinking the double helix by bending deformation

30 September 2017

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30 September 2017

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

30 September 2017

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DNA and its counterions: a molecular dynamics study

30 September 2017

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Theoretical methods for the simulation of nucleic acids.

30 September 2017

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DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

30 September 2017

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Torsional directed walks, entropic elasticity, and DNA twist stiffness

30 September 2017

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Dielectric response of triplex DNA in ionic solution from simulations

30 September 2017

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Crystal structure analysis of a complete turn of B-DNA

30 September 2017

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The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions

30 September 2017

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All-atom crystal simulations of DNA and RNA duplexes

30 September 2017

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Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

28 June 2018

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Exploring polymorphisms in B-DNA helical conformations.

28 June 2018

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28 June 2018

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On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

28 June 2018

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

28 June 2018

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Dynamics of B-DNA on the microsecond time scale.

21 September 2018

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Sequence-dependent elastic properties of DNA.

21 September 2018

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Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.

21 September 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

21 January 2018

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https://api.crossref.org/works/10.1038%2FNMETH.3658

MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNMETH.3658

Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions

21 January 2018

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Basis-set convergence in correlated calculations on Ne, N2, and H2O

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

On the absence of intrahelical DNA dynamics on the μs to ms timescale

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

The missing term in effective pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Essential dynamics of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

NMR: prediction of molecular alignment from structure using the PALES software.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

The Protein Data Bank. A computer-based archival file for macromolecular structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

X-ray and NMR Studies of the DNA Oligomer d(ATATAT): Hoogsteen Base Pairing in Duplex DNA†

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

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

21 January 2018

1 reference

12 December 2020

Optimised parameters for A-DNA and B-DNA

1 reference

12 December 2020

Length Scale Dependence of DNA Mechanical Properties

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

7 January 2021

Tautomerism and Protonation of Guanine and Cytosine. Implications in the Formation of Hydrogen-Bonded Complexes

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

7 January 2021

Basis-set convergence of the energy in molecular Hartree–Fock calculations

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

7 January 2021

Extension of the MST model to the IEF formalism: HF and B3LYP parametrizations

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

7 January 2021

Exploring the Essential Dynamics of B-DNA

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

7 January 2021

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3658

7 January 2021

Identifiers

DOI

10.1038/NMETH.3658

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Dimensions Publication ID

14 August 2017

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14 August 2017

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