Molecular modelling of cation–π interactions

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Substituent Effects on Non-Covalent Interactions with Aromatic Rings: Insights from Computational Chemistry

(2011) Rajesh K. Raju et al.   CHEMPHYSCHEM

Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals

(2011) Michael J. Schnieders et al.   Journal of Chemical Theory and Computation

Cation−π and π–π Interactions in Aqueous Solution Studied Using Polarizable Potential Models

(2011) Esam A. Orabi et al.   Journal of Chemical Theory and Computation

Quantitative Assessment of Substituent Effects on Cation−π Interactions Using Molecular Electrostatic Potential Topography

(2011) Fareed Bhasha Sayyed et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Electrostatic Polarization Is Crucial in Reproducing Cu(I) Interaction Energies and Hydration

(2011) Sergei Y. Ponomarev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily

(2011) U. Akgun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cation-π and anion-π interactions

(2011) Antonio Frontera et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Polarizable Atomic Multipole X-Ray Refinement: Hydration Geometry and Application to Macromolecules

(2010) Timothy D. Fenn et al.   BIOPHYSICAL JOURNAL

Massively parallel molecular dynamics simulations of lysozyme unfolding

(2010) R. Zhou et al.   IBM JOURNAL OF RESEARCH AND DEVELOPMENT

Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry

(2010) Valérie Campagna-Slater et al.   Journal of Chemical Information and Modeling

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

Substrate Recognition in theEscherichia coliAmmonia Channel AmtB: A QM/MM Investigation

(2010) Thomas P. Nygaard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

Finding Inspiration in the Protein Data Bank to Chemically Antagonize Readers of the Histone Code

(2010) Valérie Campagna-Slater et al.   Molecular Informatics

Transport mechanisms in the ammonium transporter family

(2010) G. Lamoureux et al.   TRANSFUSION CLINIQUE ET BIOLOGIQUE

Polarizable atomic multipole X-ray refinement: application to peptide crystals

(2009) Michael J. Schnieders et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Design of Highly Stabilized β-Hairpin Peptides through Cation−π Interactions of Lysine andN-Methyllysine with an Aromatic Pocket†

(2009) Alexander J. Riemen et al.   BIOCHEMISTRY

Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

The cooperativity of cation–π and π–π interactions

(2009) Dolly Vijay et al.   CHEMICAL PHYSICS LETTERS

Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions

(2009) Fabien Archambault et al.   Journal of Chemical Theory and Computation

Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes

(2009) Steven E. Wheeler et al.   Journal of Chemical Theory and Computation

An electrostatic interaction between TEA and an introduced pore aromatic drives spring-in-the-door inactivation inShakerpotassium channels

(2009) Christopher A. Ahern et al.   JOURNAL OF GENERAL PHYSIOLOGY

It's spring-time for slow inactivation

(2009) Riccardo Olcese   JOURNAL OF GENERAL PHYSIOLOGY

Potential Energy Curves for Cation−π Interactions: Off-Axis Configurations Are Also Attractive

(2009) Michael S. Marshall et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Functional Role of Asp160 and the Deprotonation Mechanism of Ammonium in theEscherichia coliAmmonia Channel Protein AmtB

(2009) Yuchun Lin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Explicit Solvent Effect on Cation−π Interactions: A First Principle Investigation

(2009) J. Srinivasa Rao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evaluation of stabilization energies in π–π and cation–π interactions involved in biological macromolecules byab initiocalculations

(2009) Masaru Tateno et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Polarization effects in molecular mechanical force fields

(2009) Piotr Cieplak et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Substituent Effects in Cation/π Interactions and Electrostatic Potentials above the Centers of Substituted Benzenes Are Due Primarily to Through-Space Effects of the Substituents

(2009) Steven E. Wheeler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Functional Roles of a Structural Element Involving Na+-π Interactions in the Catalytic Site of T1 Lipase Revealed by Molecular Dynamics Simulations

(2009) Yohsuke Hagiwara et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Nicotine binding to brain receptors requires a strong cation–π interaction

(2009) Xinan Xiu et al.   NATURE

Probing the role of the cation-  interaction in the binding sites of GPCRs using unnatural amino acids

(2009) M. M. Torrice et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

(2009) Pedro E. M. Lopes et al.   THEORETICAL CHEMISTRY ACCOUNTS

Efficacy of external tetraethylammonium block of the KcsA potassium channel: Molecular and Brownian dynamics studies

(2008) David Bisset et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator

(2008) Pedro E. M. Lopes et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Cation-  Interaction in the Binding Site of the Glycine Receptor Is Mediated by a Phenylalanine Residue

(2008) S. A. Pless et al.   JOURNAL OF NEUROSCIENCE

Cation-π interaction: to stack or to spread

(2008) Brijesh Kumar Mishra et al.   MOLECULAR PHYSICS

Induction effects in metal cation–benzene complexes

(2008) Ignacio Soteras et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Substrate binding, deprotonation, and selectivity at the periplasmic entrance of theEscherichia coliammonia channel AmtB

(2008) Arnaud Javelle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing

(2007) Mingyang Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

The geometry and efficacy of cation-π interactions in a diagonal position of a designed β-hairpin

(2003) Chad D. Tatko et al.   PROTEIN SCIENCE