Improved Modeling of Cation‐π and Anion‐Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins

Development and Testing of the OPLS-AA/M Force Field for RNA

(2019) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

A Comprehensive Analysis of Anion–Quadrupole Interactions in Protein Structures

(2018) Suvobrata Chakravarty et al.   BIOCHEMISTRY

Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations

(2018) Nicolas Panel et al.   BIOPHYSICAL JOURNAL

Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator

(2018) Fang-Yu Lin et al.   Journal of Chemical Theory and Computation

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

(2018) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cation−π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution

(2018) Esam A. Orabi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved Modeling of Halogenated Ligand–Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields

(2018) Fang-Yu Lin et al.   Journal of Chemical Information and Modeling

Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field

(2018) Hanif M. Khan et al.   Journal of Chemical Theory and Computation

Polarizable force field for RNA based on the classical drude oscillator

(2018) Justin A. Lemkul et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling induction phenomena in amino acid cation–$$\pi $$π interactions

(2018) Chetan Raj Rupakheti et al.   THEORETICAL CHEMISTRY ACCOUNTS

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

(2017) Justin A. Lemkul et al.   Journal of Chemical Theory and Computation

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

(2017) Hui Li et al.   Journal of Chemical Theory and Computation

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

(2017) Meagan C. Small et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The Cation-π Interaction in Small-Molecule Catalysis

(2016) C. Rose Kennedy et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

Improving the Force Field Description of Tyrosine–Choline Cation−π Interactions: QM Investigation of Phenol–N(Me)4+ Interactions

(2016) Hanif M. Khan et al.   Journal of Chemical Theory and Computation

Assessing the Current State of Amber Force Field Modifications for DNA

(2016) Rodrigo Galindo-Murillo et al.   Journal of Chemical Theory and Computation

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

A thorough anion–π interaction study in biomolecules: on the importance of cooperativity effects

(2016) Xavier Lucas et al.   Chemical Science

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

(2015) Madhurima Jana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Anion–π interactions in protein–porphyrin complexes

(2015) Mario V. Zlatović et al.   RSC Advances

Polarizable force fields for molecular dynamics simulations of biomolecules

(2015) Christopher M. Baker   Wiley Interdisciplinary Reviews-Computational Molecular Science

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

All-atom polarizable force field for DNA based on the classical drude oscillator model

(2014) Alexey Savelyev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

(2014) Jing Huang et al.   Journal of Physical Chemistry Letters

The multiple roles of histidine in protein interactions

(2013) Si-Ming Liao et al.   Chemistry Central Journal

Six-site polarizable model of water based on the classical Drude oscillator

(2013) Wenbo Yu et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

(2013) Janamejaya Chowdhary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

(2012) Yun Luo et al.   FARADAY DISCUSSIONS

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

(2012) Maria M. Reif et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

STAAR: Statistical analysis of aromatic rings

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

Molecular Dynamics of β-Hairpin Models of Epigenetic Recognition Motifs

(2012) Xiange Zheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Comparing reduced partial charge models with polarizable simulations of ionic liquids

(2012) Christian Schröder   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A Survey of Aspartate−Phenylalanine and Glutamate−Phenylalanine Interactions in the Protein Data Bank: Searching for Anion−π Pairs

(2011) Vivek Philip et al.   BIOCHEMISTRY

Recent advances in anion–π interactions

(2011) Arturo Robertazzi et al.   CRYSTENGCOMM

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

CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling

(2011) Olgun Guvench et al.   Journal of Chemical Theory and Computation

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Development of the CHARMM Force Field for Lipids

(2011) R. W. Pastor et al.   Journal of Physical Chemistry Letters

Psi4: an open-source ab initio electronic structure program

(2011) Justin M. Turney et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Relevant Anion-π Interactions in Biological Systems: The Case of Urate Oxidase

(2010) Carolina Estarellas et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Nature of cation-π interactions and their role in structural stability of immunoglobulin proteins

(2010) I. A. Tayubi et al.   BIOCHEMISTRY-MOSCOW

Density fitting of intramonomer correlation effects in symmetry-adapted perturbation theory

(2010) Edward G. Hohenstein et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

(2010) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

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

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda 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

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

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

A new force field for simulating phosphatidylcholine bilayers

(2009) David Poger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field

(2008) Edward Harder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Anion-π interactions

(2007) Brandi L. Schottel et al.   CHEMICAL SOCIETY REVIEWS