Recent advances in the study of nucleic acid flexibility by molecular dynamics

scientific article published on 04 March 2008

Recent advances in the study of nucleic acid flexibility by molecular dynamics is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

External links are
P356DOI10.1016/J.SBI.2008.01.005
P698PubMed publication ID18304803

P50authorAgnes NoyQ54636105
Modesto OrozcoQ63487839
P2093author name stringAlberto Pérez
P433issue2
P304page(s)185-193
P577publication date2008-03-04
P1433published inCurrent Opinion in Structural BiologyQ15758416
P1476titleRecent advances in the study of nucleic acid flexibility by molecular dynamics
P478volume18

Reverse relations

cites work (P2860)
Q34481643A coarse-grained model of DNA with explicit solvation by water and ions
Q37279310A mesoscale model of DNA and its renaturation
Q92761503A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
Q51258695A sequence-dependent rigid-base model of DNA.
Q38795340A single nucleotide resolution model for large-scale simulations of double stranded DNA.
Q33566434A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Q42409445Analysis of a DNA simulation model through hairpin melting experiments.
Q38237566Atomistic-level portrayal of drug-DNA Interplay: a history of courtships and meetings revealed by molecular simulations
Q42086540Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine
Q37475602Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations
Q36561838Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis
Q35075570CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
Q37626128Classical electrostatics for biomolecular simulations
Q40152255Coarse-grained modelling of supercoiled RNA.
Q29619983Conformational analysis of nucleic acids revisited: Curves+
Q37461649Constraint counting on RNA structures: linking flexibility and function
Q37235314Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition
Q42556239Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.
Q57954880Dependence of A-RNA simulations on the choice of the force field and salt strength
Q30484039Dissociation of minor groove binders from DNA: insights from metadynamics simulations
Q37373429Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations
Q38848165Evaluation of DNA Force Fields in Implicit Solvation
Q40623105Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme
Q51668649HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations
Q42092575How accurate are accurate force-fields for B-DNA?
Q42143339Impact of methylation on the physical properties of DNA.
Q33978044Is N-acetyl-D-glucosamine a rigid 4C1 chair?
Q37624617Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop
Q30457533Mesoscopic model parametrization of hydrogen bonds and stacking interactions of RNA from melting temperatures.
Q37477496Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A⋅A base pairing and a putative structure of the coralyne-induced homo-adenine duplex
Q35017031Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method
Q30383681Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity.
Q37639277Molecular recognition of RNA: challenges for modelling interactions and plasticity
Q34728020NAFlex: a web server for the study of nucleic acid flexibility.
Q27678463Non-specific protein-DNA interactions control I-CreI target binding and cleavage
Q37442208Nuance in the double-helix and its role in protein-DNA recognition.
Q51722766On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations.
Q41476736Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.
Q38389887Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
Q41957783Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations
Q42136357Robust analysis of synthetic label-free DNA junctions in solution by X-ray scattering and molecular simulation
Q35562046Selective inhibition of miR-21 by phage display screened peptide
Q35857012Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence
Q52598540Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations.
Q47429571Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations
Q38333766Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations
Q34323341The ABCs of molecular dynamics simulations on B-DNA, circa 2012.
Q34555663The effect of a G:T mispair on the dynamics of DNA
Q21134614The role of methylation in the intrinsic dynamics of B- and Z-DNA
Q37122090Unravelling the hidden DNA structural/physical code provides novel insights on promoter location
Q28476187Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites
Q48115185iMod: multipurpose normal mode analysis in internal coordinates
Q34510040μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Search more.