Molecular dynamics simulations of nucleic acid-protein complexes.
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Understanding nucleic acid-ion interactionsNon-specific protein-DNA interactions control I-CreI target binding and cleavageRecent Developments and Applications of the CHARMM force fieldsConformational analysis of nucleic acids revisited: Curves+Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach.A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong armRecognition of methylated DNA through methyl-CpG binding domain proteins.End-to-end attraction of duplex DNA.Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.Molecular Mechanism of Binding between 17β-Estradiol and DNA.Cooperativity dominates the genomic organization of p53-response elements: a mechanistic viewInvestigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes.MATCH: an atom-typing toolset for molecular mechanics force fields.The ABCs of molecular dynamics simulations on B-DNA, circa 2012.A coarse-grained model of DNA with explicit solvation by water and ions.On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics.Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study.Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structuresDynamic mechanisms for pre-miRNA binding and export by Exportin-5.The binding process of a nonspecific enzyme with DNA.do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.Effects of conformational ordering on protein/polyelectrolyte electrostatic complexation: ionic binding and chain stiffeningDNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequenceToward understanding the conformational dynamics of RNA ligationA novel implicit solvent model for simulating the molecular dynamics of RNAConstructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.Nuance in the double-helix and its role in protein-DNA recognition.Experimental and computational determination of tRNA dynamics.Molecular recognition of RNA: challenges for modelling interactions and plasticity.Conformational averaging in structural biology: issues, challenges and computational solutions.Foundations for modeling the dynamics of gene regulatory networks: a multilevel-perspective review.Atomistic-level portrayal of drug-DNA Interplay: a history of courtships and meetings revealed by molecular simulations.Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator modelInsights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis.Molecular modeling of nucleic Acid structure: electrostatics and solvation.3D-footprint: a database for the structural analysis of protein-DNA complexes.Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations.
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P2860
Molecular dynamics simulations of nucleic acid-protein complexes.
description
article científic
@ca
article scientifique
@fr
articolo scientifico
@it
artigo científico
@pt
bilimsel makale
@tr
scientific article published on 20 February 2008
@en
vedecký článok
@sk
vetenskaplig artikel
@sv
videnskabelig artikel
@da
vědecký článek
@cs
name
Molecular dynamics simulations of nucleic acid-protein complexes.
@en
Molecular dynamics simulations of nucleic acid-protein complexes.
@nl
type
label
Molecular dynamics simulations of nucleic acid-protein complexes.
@en
Molecular dynamics simulations of nucleic acid-protein complexes.
@nl
prefLabel
Molecular dynamics simulations of nucleic acid-protein complexes.
@en
Molecular dynamics simulations of nucleic acid-protein complexes.
@nl
P2860
P1476
Molecular dynamics simulations of nucleic acid-protein complexes
@en
P2093
Alexander D Mackerell
P2860
P304
P356
10.1016/J.SBI.2007.12.012
P577
2008-02-20T00:00:00Z