(Q36428161)

14 August 2017

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

1 reference

14 August 2017

1 reference

18

David A Case

0 references

Alexandra Balaceanu

Alexandra Balaceanu

10

0 references

Federica Battistini

Federica Battistini

12

0 references

Pablo D. Dans

Pablo D Dans

2

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Agnes Noy

Agnes Noy

3

0 references

Ignacio Faustino

Ignacio Faustino

5

0 references

Guillem Portella

Guillem Portella

11

0 references

Josep Lluís Gelpí

Josep Lluis Gelpí

13

0 references

Carlos González

Carlos González

14

0 references

Michele Vendruscolo

15

Michele Vendruscolo

1 reference

14 August 2017

17

Sarah A Harris

1 reference

14 August 2017

Alberto Pérez

4

0 references

Modesto Orozco

19

Modesto Orozco

1 reference

14 August 2017

Ivan Ivani

1

1 reference

14 August 2017

Adam Hospital

6

1 reference

14 August 2017

Jürgen Walther

7

1 reference

14 August 2017

Pau Andrio

8

1 reference

14 August 2017

Ramon Goñi

9

1 reference

14 August 2017

Charles A Laughton

16

1 reference

14 August 2017

David A Case

18

1 reference

14 August 2017

16 November 2015

1 reference

full work available at URL

14 August 2017

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

content deliverer

White Rose Research Online

0 references

published in

Nature Methods

1 reference

14 August 2017

13

1 reference

14 August 2017

1

1 reference

14 August 2017

55-58

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Direct measurement of the dielectric polarization properties of 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=4700514

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

NAFlex: a web server for the study of nucleic acid flexibility.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

ACPYPE - AnteChamber PYthon Parser interfacE

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Frontiers in molecular dynamics simulations of 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=4700514

A measure of bending in nucleic acids structures applied to A-tract 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=4700514

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Conformational analysis of nucleic acids revisited: Curves+

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Towards a molecular dynamics consensus view of B-DNA flexibility

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Kinking the double helix by bending deformation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

DNA and its counterions: a molecular dynamics study

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Theoretical methods for the simulation of nucleic acids.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Torsional directed walks, entropic elasticity, and DNA twist stiffness

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Dielectric response of triplex DNA in ionic solution from simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Crystal structure analysis of a complete turn of B-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=4700514

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

All-atom crystal simulations of DNA and RNA duplexes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Exploring polymorphisms in B-DNA helical conformations.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Dynamics of B-DNA on the microsecond time scale.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

Sequence-dependent elastic properties of DNA.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4700514

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

1 reference

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

1 reference

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

1 reference

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

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

1 reference

Dimensions Publication ID

14 August 2017

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0 references

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1 reference

14 August 2017

PubMed publication ID

26569599

1 reference