Assessing the Current State of Amber Force Field Modifications for DNA (Q27301352)

26 June 2017

title

Assessing the Current State of Amber Force Field Modifications for DNA (English)

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26 June 2017

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5

Michal Otyepka

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Jirí Sponer

4

object named as

Jiří Šponer

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26 June 2017

Thomas E. Cheatham, III

7

object named as

Thomas E Cheatham

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26 June 2017

author name string

Rodrigo Galindo-Murillo

1

1 reference

26 June 2017

James C Robertson

2

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26 June 2017

Marie Zgarbová

3

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26 June 2017

Petr Jurečka

6

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26 June 2017

language of work or name

English

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publication date

14 June 2016

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Journal of Chemical Theory and Computation

26 June 2017

published in

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26 June 2017

volume

12

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26 June 2017

issue

8

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26 June 2017

page(s)

4114-4127

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Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

26 June 2017

cites work

1 reference

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B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

21 March 2017

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

21 March 2017

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Solution structure of an A-tract DNA bend

21 March 2017

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Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

21 March 2017

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Structure of a B-DNA dodecamer: conformation and dynamics

21 March 2017

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

21 March 2017

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Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

28 September 2017

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Improved Force Field Parameters Lead to a Better Description of RNA Structure

28 September 2017

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

28 September 2017

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μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

28 September 2017

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Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

28 September 2017

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Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods

28 September 2017

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Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

28 September 2017

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Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.

28 September 2017

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Automatic workflow for the classification of local DNA conformations

28 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.

28 September 2017

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

28 September 2017

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The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

28 September 2017

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The ABCs of molecular dynamics simulations on B-DNA, circa 2012.

28 September 2017

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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

28 September 2017

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

28 September 2017

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28 September 2017

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31P NMR investigation of backbone dynamics in DNA binding sites

28 September 2017

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28 September 2017

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28 September 2017

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A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data

28 September 2017

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28 September 2017

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Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA.

28 September 2017

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

28 September 2017

1 reference

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Timeline: Z-DNA: the long road to biological function

28 September 2017

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

28 September 2017

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

28 September 2017

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Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC)

28 September 2017

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The effect of crystal packing on oligonucleotide double helix structure

28 September 2017

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Proton exchange and base-pair opening kinetics in 5'-d(CGCGAATTCGCG)-3' and related dodecamers

28 September 2017

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Effects of sequence and length on imino proton exchange and base pair opening kinetics in DNA oligonucleotide duplexes

28 September 2017

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DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations

28 September 2017

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Long-timescale dynamics of the Drew-Dickerson dodecamer.

28 September 2017

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Building Water Models: A Different Approach

31 May 2018

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31 May 2018

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

31 May 2018

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31 May 2018

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Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters

31 May 2018

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31 May 2018

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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

31 May 2018

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Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

28 November 2018

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Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

28 November 2018

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Charge hydration asymmetry: the basic principle and how to use it to test and improve water models

28 November 2018

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Kinking occurs during molecular dynamics simulations of small DNA minicircles.

28 November 2018

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

28 November 2018

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An improved nucleic acid parameter set for the GROMOS force field

28 November 2018

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Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

28 November 2018

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

28 November 2018

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12 December 2020

Polymorphism of a synthetic DNA in solution

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12 December 2020

Large-amplitude fast motions in double-stranded DNA driven by solvent thermal fluctuations

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12 December 2020

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

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A single mode of DNA base-pair opening drives imino proton exchange

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12 December 2020

Identifiers

DOI

10.1021/ACS.JCTC.6B00186

1 reference

release_5dtmrantwndrdfoijplr3u4htm

26 June 2017

Fatcat ID

0 references

OpenCitations bibliographic resource ID

1324620

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1324620

1 reference