(Q38052698)

English

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

scientific article published on 16 October 2012

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scholarly article

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Europe PubMed Central

PubMed publication ID

27 August 2017

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

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

structural biology

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based on heuristic

inferred from title

quantum biology

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based on heuristic

inferred from title

8

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Europe PubMed Central

PubMed publication ID

27 August 2017

object named as

Daniel Svozil

4

0 references

6

object named as

Pavel Banáš

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

1

object named as

Jiří Šponer

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

author name string

Arnošt Mládek

2

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Europe PubMed Central

PubMed publication ID

27 August 2017

Judit E Šponer

3

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

Marie Zgarbová

5

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Europe PubMed Central

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27 August 2017

Petr Jurečka

7

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Europe PubMed Central

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27 August 2017

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publication date

16 October 2012

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27 August 2017

Physical Chemistry Chemical Physics

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Europe PubMed Central

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27 August 2017

14

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Europe PubMed Central

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27 August 2017

44

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

15257-15277

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

The DNA Helix and How it is Read

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Working the kinks out of nucleosomal DNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Quadruplex DNA: sequence, topology and structure

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Prediction of RNA secondary structure by free energy minimization

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The UA_handle: a versatile submotif in stable RNA architectures

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The non-Watson-Crick base pairs and their associated isostericity matrices

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Classification and energetics of the base-phosphate interactions in RNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

RNA structure: reading the ribosome

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Nature and magnitude of aromatic stacking of nucleic acid bases

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

RNA backbone is rotameric

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

DNA conformations and their sequence preferences.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

1 reference

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21 January 2018

DNA bending: the prevalence of kinkiness and the virtues of normality

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Two distinct modes of protein-induced bending in DNA.

1 reference

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21 January 2018

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA.

1 reference

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21 January 2018

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A standard reference frame for the description of nucleic acid base-pair geometry.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

NMR spectroscopy of RNA.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

PROSIT: pseudo-rotational online service and interactive tool, applied to a conformational survey of nucleosides and nucleotides.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Alpha/gamma transitions in the B-DNA backbone

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Crystal structure of parallel quadruplexes from human telomeric DNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Protein-DNA interactions: A structural analysis

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A-form conformational motifs in ligand-bound DNA structures

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Protein-DNA interaction. No code for recognition

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Nuance in the double-helix and its role in protein-DNA recognition.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

RNA conformational classes

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The crystal structure of a 26-nucleotide RNA containing a hook-turn

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Stepping through an RNA structure: A novel approach to conformational analysis

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Statistical analysis of RNA backbone

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Nonparametric clustering for studying RNA conformations

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: a solution to the problem

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https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Enthalpy difference between conformations of normal alkanes: Intramolecular basis set superposition error (BSSE) in the case of n-butane and n-hexane

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

On the Correlation Problem in Atomic and Molecular Systems. Calculation of Wavefunction Components in Ursell‐Type Expansion Using Quantum‐Field Theoretical Methods

1 reference

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21 January 2018

Correlation Problems in Atomic and Molecular Systems. IV. Extended Coupled-Pair Many-Electron Theory and Its Application to the B H 3 Molecule

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Coupled-cluster theory in quantum chemistry

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Improvement of the coupled-cluster singles and doubles method via scaling same- and opposite-spin components of the double excitation correlation energy.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison w

1 reference

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21 January 2018

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Generalized Gradient Approximation Made Simple

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared withab initioquantum mechanics calculations

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other fun

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Accurate description of van der Waals complexes by density functional theory including empirical corrections

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions

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https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Density-functional thermochemistry. III. The role of exact exchange

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https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

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https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions

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21 January 2018

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

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21 January 2018

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Kinetics and thermodynamics of the formation of glucose arsenate. Reaction of glucose arsenate with phosphoglucomutase

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https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Backbone modification of nucleic acids: synthesis, structure and therapeutic applications.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Synthetic genetic polymers capable of heredity and evolution

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21 January 2018

Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3'-->2') oligonucleotide system

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21 January 2018

A simple glycol nucleic acid

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21 January 2018

Solution structure of a HNA-RNA hybrid

1 reference

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21 January 2018

Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex

1 reference

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21 January 2018

How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The kink-turn: a new RNA secondary structure motif

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Crystal structure of the ribosomal RNA domain essential for binding elongation factors

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Molecular dynamics simulations of sarcin-ricin rRNA motif.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The chemical versatility of RNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

The chemical origins of life and its early evolution: an introduction

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Modulating RNA structure and catalysis: lessons from small cleaving ribozymes

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Autolytic processing of dimeric plant virus satellite RNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Control of gene expression by a natural metabolite-responsive ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

HDV-like self-cleaving ribozymes

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Widespread occurrence of self-cleaving ribozymes

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Trapped water molecules are essential to structural dynamics and function of a ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Structural roles of monovalent cations in the HDV ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A conformational switch controls hepatitis delta virus ribozyme catalysis

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

General acid catalysis by the hepatitis delta virus ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights?

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Charged nucleobases and their potential for RNA catalysis

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Relationship between internucleotide linkage geometry and the stability of RNA.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

A view at the millennium: the efficiency of enzymatic catalysis

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Ground State and Transition State Contributions to the Rates of Intramolecular and Enzymatic Reactions

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

How much do enzymes really gain by restraining their reacting fragments?

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Frontiers in molecular dynamics simulations of DNA.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Force field parameters for rotation around chi torsion axis in nucleic acids

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Examination by the molecular orbital method of the intrinsic conformation preferences of nucleic acid sequence

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Conformational studies of nucleic acids. II. The conformational energetics of commonly occurring nucleosides

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Quantum chemical studies on the conformational structure of nucleic acids. IV. Calculation of backbone structure by CNDO method.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Backbone Conformations in Secondary and Tertiary Structural Units of Nucleic Acids. Constraint in the Phosphodiester Conformation

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Reevaluation of Stereoelectronic Contributions to the Conformational Properties of the Phosphodiester and N3‘-Phosphoramidate Moieties of Nucleic Acids

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Intramolecular hydrogen bonding in 2′-deoxyribonucleosides: an AIM topological study of the electronic density

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Intramolecular hydrogen bonding in ribonucleosides: an AIM topological study of the electronic densityElectronic supplementary information (ESI) available: Integrated properties of atomic basins, radii characterizing hydrogen bond interactions, and p

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Dependence of deformability of geometries and characteristics of intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides on DNA conformations

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

DFT study of B-like conformations of deoxydinucleoside monophosphates containing Gua and/or Cyt and their complexes with Na+ cation

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Conformational analysis of canonical 2-deoxyribonucleotides. 1. Pyrimidine nucleotides

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides: an atoms in molecules study

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Conformational flexibility of c8-phenoxyl-2'-deoxyguanosine nucleotide adducts

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Calculating the response of NMR shielding tensor σ(31P) and 2J(31P,13C) coupling constants in nucleic acid phosphate to coordination of the Mg2+ cation

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Effect of local sugar and base geometry on 13C and 15N magnetic shielding anisotropy in DNA nucleosides

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Phosphorus chemical shifts in a nucleic acid backbone from combined molecular dynamics and density functional calculations

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Structural interpretation of J coupling constants in guanosine and deoxyguanosine: modeling the effects of sugar pucker, backbone conformation, and base pairing.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

DNA strand breaks induced by near-zero-electronvolt electron attachment to pyrimidine nucleotides

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Electron attachment-induced DNA single-strand breaks at the pyrimidine sites

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Electron attachment to DNA single strands: gas phase and aqueous solution

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Low-energy electron attachment to 5'-thymidine monophosphate: modeling single strand breaks through dissociative electron attachment.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP.

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

On the convergence of the (ΔECCSD(T)−ΔEMP2) term for complexes with multiple H-bonds

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Geometry of the Phosphate Group and Its Interactions with Metal Cations in Crystals andab InitioCalculations

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41987D

21 January 2018

Identifiers

10.1039/C2CP41987D

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

27 August 2017

ResearchGate publication ID

0 references

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