Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.
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Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations.Stacking in RNA: NMR of Four Tetramers Benchmark Molecular DynamicsReliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.The impact of base stacking on the conformations and electrostatics of single-stranded DNA.Visualizing single-stranded nucleic acids in solution.The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics.Computational study of unfolding and regulation mechanism of preQ1 riboswitches.Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion.TRANSCRIPTION. Allosteric transcriptional regulation via changes in the overall topology of the core promoter.Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on ChromatinMultidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.Molecular modeling of nucleic Acid structure: setup and analysis.Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.Twenty-five years of nucleic acid simulationsLarge-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics SimulationsEmpirical Corrections to the Amber RNA Force Field with Target Metadynamics.Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Physics-based all-atom modeling of RNA energetics and structure.RNA force field with accuracy comparable to state-of-the-art protein force fields.AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations.Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.
P2860
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P2860
Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.
description
2011 nî lūn-bûn
@nan
2011年の論文
@ja
2011年論文
@yue
2011年論文
@zh-hant
2011年論文
@zh-hk
2011年論文
@zh-mo
2011年論文
@zh-tw
2011年论文
@wuu
2011年论文
@zh
2011年论文
@zh-cn
name
Benchmarking AMBER force field ...... mproved by revised χ torsions.
@en
type
label
Benchmarking AMBER force field ...... mproved by revised χ torsions.
@en
prefLabel
Benchmarking AMBER force field ...... mproved by revised χ torsions.
@en
P2093
P2860
P356
P1476
Benchmarking AMBER force field ...... mproved by revised χ torsions.
@en
P2093
Harry A Stern
Ilyas Yildirim
Jason D Tubbs
Scott D Kennedy
P2860
P304
P356
10.1021/JP2016006
P407
P577
2011-07-01T00:00:00Z