How accurate are accurate force-fields for B-DNA?

scientific article published on 13 January 2017

How accurate are accurate force-fields for B-DNA? is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1093/NAR/GKW1355
P932PMC publication ID5397185
P698PubMed publication ID28088759

P50authorModesto OrozcoQ63487839
Adam HospitalQ79137384
Carlos GonzálezQ40859618
Guillem PortellaQ41047555
P2093author name stringPablo D Dans
Ivan Ivani
P2860cites workStructure of a B-DNA dodecamer: conformation and dynamicsQ24635075
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Assessing the Current State of Amber Force Field Modifications for DNAQ27301352
Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNAQ27324521
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Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactionsQ27633340
Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairingQ27638194
Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropyQ27641450
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanesQ29397708
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DNA sequence-dependent deformability deduced from protein-DNA crystal complexesQ29616629
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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNAQ57954801
Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methodsQ70181047
Optimised parameters for A-DNA and B-DNAQ70409700
Computer simulation of DNA double-helix dynamicsQ70905187
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeatQ77366872
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Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNAQ34312985
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Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids.Q34427261
On the absence of intrahelical DNA dynamics on the μs to ms timescaleQ34433149
cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNAQ34489622
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNAQ34510040
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High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMDQ34973102
Theoretical methods for the simulation of nucleic acids.Q35606425
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.Q36422866
Parmbsc1: a refined force field for DNA simulationsQ36428161
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Multiscale simulation of DNA.Q38680648
Twenty-five years of nucleic acid simulationsQ39399632
The structural impact of DNA mismatchesQ40176435
Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.Q40297201
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.Q41476736
Long-timescale dynamics of the Drew-Dickerson dodecamer.Q41931128
Exploring polymorphisms in B-DNA helical conformations.Q42370883
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator modelQ42404600
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field ParametersQ42627952
Dynamics of B-DNA on the microsecond time scale.Q50141941
P275copyright licenseCreative Commons Attribution-NonCommercial 4.0 InternationalQ34179348
P6216copyright statuscopyrightedQ50423863
P4510describes a project that usesggplot2Q326489
P433issue7
P304page(s)4217-4230
P577publication date2017-01-13
P1433published inNucleic Acids ResearchQ135122
P1476titleHow accurate are accurate force-fields for B-DNA?
P478volume45

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