(Q40164438)

English

DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar.

scientific article published on 17 April 2014

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24744240%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar (English)

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24744240%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

1

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14 March 2020

author name string

Jennifer L Kellie

2

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14 March 2020

Stacey D Wetmore

3

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14 March 2020

publication date

17 April 2014

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14 March 2020

Nucleic Acids Research

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14 March 2020

42

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14 March 2020

10

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14 March 2020

6726-6741

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14 March 2020

copyright license

Creative Commons Attribution 3.0 Unported

10 November 2016

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April 2022 Public Data File from Crossref

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0 references

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Origins of specificity in protein-DNA recognition.

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A preliminary investigation of the additivity of pi-pi or pi+-pi stacking and T-shaped interactions between natural or damaged DNA nucleobases and histidine

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Nature and magnitude of aromatic stacking of nucleic acid bases

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Sugars stack up.

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The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections

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Role of aromatic amino acids in protein-nucleic acid recognition.

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Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure

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Role of CH/pi interactions in substrate binding by Escherichia coli beta-galactosidase.

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Aromatic side-chain interactions in proteins. Near- and far-sequence His-X pairs

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Aromatic side-chain interactions in proteins. II. Near- and far-sequence Phe-X pairs

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Aromatic side-chain interactions in proteins. I. Main structural features

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Variability in the pKa of histidine side-chains correlates with burial within proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4041443

20 August 2018

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4041443

20 August 2018

Dispersion interactions of carbohydrates with condensate aromatic moieties: Theoretical study on the CH–π interaction additive properties

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4041443

20 August 2018

Mercury CSD 2.0– new features for the visualization and investigation of crystal structures

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Basis-set convergence in correlated calculations on Ne, N2, and H2O

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Computational clues for a new mechanism in the glycosylase activity of the human DNA repair protein hOGG1. A generalized paradigm for purine-repairing systems?

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Comprehensive Energy Analysis for Various Types of π-Interaction

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

STAAR: Statistical analysis of aromatic rings

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Noncovalent interactions in biochemistry

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Highly Polar Carbohydrates Stack onto DNA Duplexes via CH/π Interactions

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Apolar carbohydrates as DNA capping agents

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Potential Energy Surface of the Cytosine Dimer: MP2 Complete Basis Set Limit Interaction Energies, CCSD(T) Correction Term, and Comparison with the AMBER Force Field

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU269

21 January 2018

Carbohydrate-aromatic interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effects of extending the computational model on DNA-protein T-shaped interactions: the case of adenine-histidine dimers

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Carbohydrate molecular recognition: a spectroscopic investigation of carbohydrate-aromatic interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

From gene expression to disease risk

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Characterization of nucleobase-amino acid stacking interactions utilized by a DNA repair enzyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

C-H...pi-interactions in proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Histidine-Aromatic Interactions in Proteins and Protein-Ligand Complexes: Quantum Chemical Study of X-ray and Model Structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluating how discrete water molecules affect protein-DNA π-π and π(+)-π stacking and T-shaped interactions: the case of histidine-adenine dimers

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Combined effects of π-π stacking and hydrogen bonding on the (N1) acidity of uracil and hydrolysis of 2'-deoxyuridine

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Aromatic-Aromatic Interactions Database, A(2)ID: an analysis of aromatic π-networks in proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Exploration of CH···π mediated stacking interactions in saccharide: aromatic residue complexes through conformational sampling

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein-RNA interactions: structural analysis and functional classes

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evidence for Stabilization of DNA/RNA-Protein Complexes Arising from Nucleobase-Amino Acid Stacking and T-Shaped Interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

1 reference

https://pubmed.ncbi.nlm.nih.gov/24744240

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKU269

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24744240%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

release_xsjddd72mzhojg7p3ikt6sqp6u

1 reference

https://api.fatcat.wiki/v0/release/xsjddd72mzhojg7p3ikt6sqp6u

24 November 2022

based on heuristic

mapped directly with Wikidata item

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24744240%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24744240%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

ResearchGate publication ID

0 references

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