(Q38112952)

29 August 2017

title

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists (English)

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29 August 2017

main subject

computational biology

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6

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29 August 2017

4

Pavel Banáš

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29 August 2017

1

Jiří Šponer

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29 August 2017

Judit E Šponer

2

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29 August 2017

Arnošt Mládek

series ordinal

3

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29 August 2017

Petr Jurečka

series ordinal

5

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29 August 2017

publication date

7 June 2013

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29 August 2017

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29 August 2017

volume

64

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29 August 2017

issue

1

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29 August 2017

page(s)

3-11

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Calculations of nucleic acid conformations

29 August 2017

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The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

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7 January 2021

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The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing

7 January 2021

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7 January 2021

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7 January 2021

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Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding

7 January 2021

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Calculation of the binding free energy for magnesium-RNA interactions

7 January 2021

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7 January 2021

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7 January 2021

Polarizable force fields

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A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

7 January 2021

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The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

7 January 2021

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Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

7 January 2021

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Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

7 January 2021

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Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

7 January 2021

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Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

7 January 2021

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Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

7 January 2021

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Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

7 January 2021

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Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

7 January 2021

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Insights into intrastrand cross-link lesions of DNA from QM/MM molecular dynamics simulations.

7 January 2021

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QM/MM description of platinum–DNA interactions: comparison of binding and DNA distortion of five drugs

7 January 2021

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Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode

7 January 2021

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Classification and energetics of the base-phosphate interactions in RNA

7 January 2021

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Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs

7 January 2021

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Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment

7 January 2021

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Quantum-mechanical analysis of the energetic contributions to π stacking in nucleic acids versus rise, twist, and slide

7 January 2021

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Guanine base stacking in G-quadruplex nucleic acids

7 January 2021

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Density Functionals with Broad Applicability in Chemistry

7 January 2021

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Dispersion-corrected density functional theory for aromatic interactions in complex systems

7 January 2021

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Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations

7 January 2021

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Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

7 January 2021

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DNA conformations and their sequence preferences.

7 January 2021

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Basis-set convergence of the energy in molecular Hartree–Fock calculations

7 January 2021

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10.1016/J.YMETH.2013.05.025

7 January 2021

Identifiers

DOI

1 reference

29 August 2017

1 reference