Efficient Calculation of Many Stacking and Pairing Free Energies in DNA from a Few Molecular Dynamics Simulations

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Efficient Calculation of Many Stacking and Pairing Free Energies in DNA from a Few Molecular Dynamics Simulations is …
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scholarly articleQ13442814

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P356DOI10.1002/CHEM.200401120
P698PubMed publication ID15880545

P50authorChris OostenbrinkQ30505204
Wilfred F van GunsterenQ52153822
P2860cites workMolecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic AcidQ1895685
Structure of a B-DNA dodecamer: conformation and dynamicsQ24635075
The B-DNA dodecamer at high resolution reveals a spine of water on sodiumQ27758585
Synthetically modified DNAs as substrates for polymerasesQ34096433
Structure and Base Pairing Properties of a Replicable Nonpolar Isostere for DeoxyadenosineQ34129242
Naphthalene, Phenanthrene, and Pyrene as DNA Base Analogues: Synthesis, Structure, and Fluorescence in DNA.Q34143828
Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA.Q34144275
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.Q43922829
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulationQ44706733
Bending of oligonucleotides containing an isosteric nucleobase: 7-deaza-2'-deoxyadenosine replacing dA within d(A)6 tractsQ46886593
Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and characterQ47442749
Why is it so difficult to simulate entropies, free energies, and their differences?Q49297337
An improved nucleic acid parameter set for the GROMOS force fieldQ56225273
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteinsQ56776034
Molecular dynamics with coupling to an external bathQ57569060
The GROMOS Biomolecular Simulation Program PackageQ57746723
Estimating entropies from molecular dynamics simulationsQ58005574
Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and XenoestrogensQ58005587
Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/LQ58616227
Effect of Ionizing Radiation on Adenine in Aerated and De-Aerated Aqueous SolutionsQ59090625
P433issue15
P407language of work or nameEnglishQ1860
P921main subjectgeneral chemistryQ909510
P304page(s)4340-4348
P577publication date2005-05-06
P1433published inChemistry—A European JournalQ898737
P1476titleEfficient Calculation of Many Stacking and Pairing Free Energies in DNA from a Few Molecular Dynamics Simulations
P478volume11

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cites work (P2860)
Q35124317Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings
Q50919565Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system.
Q36627376Exploring the role of large conformational changes in the fidelity of DNA polymerase beta
Q41005478Free energy analysis and mechanism of base pair stacking in nicked DNA.
Q36335325Intramolecular base stacking of dinucleoside monophosphate anions in aqueous solution
Q42734930On the stability of peptide nucleic acid duplexes in the presence of organic solvents
Q51115239On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters.
Q35212044Prechemistry versus preorganization in DNA replication fidelity
Q27657790Structural Perturbations Induced by the α-Anomer of the Aflatoxin B 1 Formamidopyrimidine Adduct in Duplex and Single-Strand DNA
Q38073986Why nature really chose phosphate

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