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

Electrochemical and Theoretical Study of π–π Stacking Interactions between Graphitic Surfaces and Pyrene Derivatives

(2014) Mengmei Cao et al.   Journal of Physical Chemistry C

Carbohydrate-DNA Interactions at G-Quadruplexes: Folding and Stability Changes by Attaching Sugars at the 5′-End

(2013) Irene Gómez-Pinto et al.   CHEMISTRY-A EUROPEAN JOURNAL

Genetics of human gene expression

(2013) Barbara E Stranger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Efficient basis sets for non-covalent interactions in XDM-corrected density-functional theory

(2013) Erin R. Johnson et al.   JOURNAL OF CHEMICAL PHYSICS

Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations

(2013) Arnošt Mládek et al.   Journal of Chemical Theory and Computation

Noncovalent Interactions of DNA Bases with Naphthalene and Graphene

(2013) Yeonchoo Cho et al.   Journal of Chemical Theory and Computation

Carbohydrate–Aromatic Interactions: Vibrational Spectroscopy and Structural Assignment of Isolated Monosaccharide Complexes with p-Hydroxy Toluene and N-Acetyl l-Tyrosine Methylamide

(2013) E. Cristina Stanca-Kaposta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Significant Strength of Charged DNA–Protein π–π Interactions: A Preliminary Study of Cytosine

(2013) Rachael A. Wells et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Examination of Tyrosine/Adenine Stacking Interactions in Protein Complexes

(2013) Kari L. Copeland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2013) Arnošt Mládek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effects of London dispersion correction in density functional theory on the structures of organic molecules in the gas phase

(2013) Stefan Grimme et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Carbohydrate–Aromatic Interactions

(2012) Juan Luis Asensio et al.   ACCOUNTS OF CHEMICAL RESEARCH

Energy Component Analysis of π Interactions

(2012) C. David Sherrill   ACCOUNTS OF CHEMICAL RESEARCH

Rational drug design for anti-cancer chemotherapy: Multi-target QSAR models for the in silico discovery of anti-colorectal cancer agents

(2012) Alejandro Speck-Planche et al.   BIOORGANIC & MEDICINAL CHEMISTRY

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

(2012) Manju Kumari et al.   CARBOHYDRATE RESEARCH

Apolar carbohydrates as DNA capping agents

(2012) Ricardo Lucas et al.   CHEMICAL COMMUNICATIONS

Protein-protein Interactions: Network Analysis and Applications in Drug Discovery

(2012) Jennyfer Bultinck et al.   CURRENT PHARMACEUTICAL DESIGN

Structural Factors That Determine Selectivity of a High Fidelity DNA Polymerase for Deoxy-, Dideoxy-, and Ribonucleotides

(2012) Weina Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Performance of Non-Local and Atom-Pairwise Dispersion Corrections to DFT for Structural Parameters of Molecules with Noncovalent Interactions

(2012) Waldemar Hujo et al.   Journal of Chemical Theory and Computation

STAAR: Statistical analysis of aromatic rings

(2012) David D. Jenkins et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessment of the Performance of MP2 and MP2 Variants for the Treatment of Noncovalent Interactions

(2012) Kevin E. Riley et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Combined Effects of π–π Stacking and Hydrogen Bonding on the (N1) Acidity of Uracil and Hydrolysis of 2′-Deoxyuridine

(2012) Jennifer L. Kellie et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Y-family DNA polymerases and their role in tolerance of cellular DNA damage

(2012) Julian E. Sale et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

(2012) Michaela Wimmerová et al.   PLoS One

A short adaptive path from DNA to RNA polymerases

(2012) C. Cozens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aromatic Rings in Chemical and Biological Recognition: Energetics and Structures

(2011) Laura M. Salonen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A QM/QM Investigation of the hUNG2 Reaction Surface: The Untold Tale of a Catalytic Residue

(2011) Jennifer L. Przybylski et al.   BIOCHEMISTRY

Unlocking the Sugar “Steric Gate” of DNA Polymerases

(2011) Jessica A. Brown et al.   BIOCHEMISTRY

Three-Dimensional Potential Energy Surface of Selected Carbohydrates’ CH/π Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods

(2011) Stanislav Kozmon et al.   CHEMISTRY-A EUROPEAN JOURNAL

Strategies in the Rational Drug Design

(2011) T. Mavromoustakos et al.   CURRENT MEDICINAL CHEMISTRY

Aromatic–Aromatic Interactions Database, A2ID: An analysis of aromatic π-networks in proteins

(2011) Mukesh Chourasia et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

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

(2011) Lori A. Burns et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2011) Jan Řezáč et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural Mechanism of Ribonucleotide Discrimination by a Y-Family DNA Polymerase

(2011) Kevin N. Kirouac et al.   JOURNAL OF MOLECULAR BIOLOGY

Magnitude and Nature of Carbohydrate–Aromatic Interactions in Fucose–Phenol and Fucose–Indole Complexes: CCSD(T) Level Interaction Energy Calculations

(2011) Seiji Tsuzuki et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Effects of Extending the Computational Model on DNA–Protein T-shaped Interactions: The Case of Adenine–Histidine Dimers

(2011) Lesley R. Rutledge et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Evaluating How Discrete Water Molecules Affect Protein–DNA π–π and π+–π Stacking and T-Shaped Interactions: The Case of Histidine-Adenine Dimers

(2011) Fern M. V. Leavens et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling the Chemical Step Utilized by Human Alkyladenine DNA Glycosylase: A Concerted Mechanism Aids in Selectively Excising Damaged Purines

(2011) Lesley R. Rutledge et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2011) Ricardo Lucas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Contribution of C-H … π Interactions to the Affinity and Specificity of Carbohydrate Binding Sites

(2011) Petety V. Balaji   MINI-REVIEWS IN ORGANIC CHEMISTRY

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

(2011) Stanislav Kozmon et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Noncovalent interactions in biochemistry

(2011) Kevin E. Riley et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

The assessment of density functionals for DNA–protein stacked and T-shaped complexes

(2010) Lesley R. Rutledge et al.   CANADIAN JOURNAL OF CHEMISTRY

MP2, density functional theory, and molecular mechanical calculations of C–H···π and hydrogen bond interactions in a cellulose-binding module–cellulose model system

(2010) Mohamed Naseer Ali Mohamed et al.   CARBOHYDRATE RESEARCH

Carbohydrate-Aromatic Interactions: The Role of Curvature on XH···π Interactions

(2010) R. Mahesh Kumar et al.   JOURNAL OF PHYSICAL CHEMISTRY A

A Preliminary Investigation of the Additivity of π−π or π+−π Stacking and T-Shaped Interactions between Natural or Damaged DNA Nucleobases and Histidine

(2010) Lesley R. Rutledge et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The DNA Damage Response: Making It Safe to Play with Knives

(2010) Alberto Ciccia et al.   MOLECULAR CELL

The effects of perfluorination on carbohydrate–π interactions: computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin

(2010) Rajesh K. Raju et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions

(2010) Claudio A. Morgado et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2010) Cassandra D. M. Churchill et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Carbohydrate–aromatic interactions: A computational and IR spectroscopic investigation of the complex, methyl α-l-fucopyranoside·toluene, isolated in the gas phase

(2009) Zheng Su et al.   CHEMICAL PHYSICS LETTERS

Systems and Synthetic biology: tackling genetic networks and complex diseases

(2009) G Cuccato et al.   HEREDITY

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

(2009) Lesley R. Rutledge et al.   Journal of Chemical Theory and Computation

Comprehensive Energy Analysis for Various Types of π-Interaction

(2009) N. Jiten Singh et al.   Journal of Chemical Theory and Computation

On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X−H···π): WFT and DFT Calculations

(2009) Kevin E. Riley et al.   Journal of Chemical Theory and Computation

Magnitude and Nature of Carbohydrate−Aromatic Interactions: Ab Initio Calculations of Fucose−Benzene Complex

(2009) Seiji Tsuzuki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Noncovalent Interactions Involving Histidine: The Effect of Charge on π−π Stacking and T-Shaped Interactions with the DNA Nucleobases

(2009) Cassandra D. M. Churchill et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Enthalpic Nature of the CH/π Interaction Involved in the Recognition of Carbohydrates by Aromatic Compounds, Confirmed by a Novel Interplay of NMR, Calorimetry, and Theoretical Calculations

(2009) Karla Ramírez-Gualito et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

Carbohydrate–aromatic π interactions: a test of density functionals and the DFT-D method

(2009) Rajesh K. Raju et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effects of the biological backbone on DNA–protein stacking interactions

(2009) Cassandra D. M. Churchill et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2008) Clare F. Macrae et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

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

(2008) Lesley R. Rutledge et al.   Journal of Chemical Theory and Computation

Calorimetric Measurement of the CH/π Interaction Involved in the Molecular Recognition of Saccharides by Aromatic Compounds

(2008) Lorena Bautista-Ibáñez et al.   JOURNAL OF ORGANIC CHEMISTRY

Probing Phenylalanine/Adenine π-Stacking Interactions in Protein Complexes with Explicitly Correlated and CCSD(T) Computations

(2008) Kari L. Copeland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Carbohydrate−π Interactions: What Are They Worth?

(2008) Zachary R. Laughrey et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sugars stack up

(2008) Chad Tatko   Nature Chemical Biology

From gene expression to disease risk

(2008) Emmanouil T Dermitzakis   NATURE GENETICS

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

(2008) Raman Sharma et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A post-SCF complete basis set study on the recognition patterns of uracil and cytosine by aromatic and π–aromatic stacking interactions with amino acid residues

(2008) Piotr Cysewski   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2008) Lesley R. Rutledge et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Controlled aggregation of adenine by sugars: physicochemical studies, molecular modelling simulations of sugar–aromatic CH–π stacking interactions, and biological significance

(2008) Marc Maresca et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Carbohydrate–protein recognition probed by density functional theory and ab initio calculations including dispersive interactions

(2008) Rajesh K. Raju et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Nature and magnitude of aromatic stacking of nucleic acid bases

(2008) Jiří Šponer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Insights into Protein–DNA Interactions through Structure Network Analysis

(2008) R. Sathyapriya et al.   PLoS Computational Biology