A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids

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

Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections

(2016) Xiangda Peng et al.   Journal of Chemical Theory and Computation

Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions

(2015) Nara Lee Chon et al.   BIOCHEMISTRY

Interfacial Water Screens the Protein-Induced Transmembrane Voltage

(2015) Piotr Zarzycki   JOURNAL OF PHYSICAL CHEMISTRY B

Revisiting the bilayer structures of fluid phase phosphatidylglycerol lipids: Accounting for exchangeable hydrogens

(2014) Jianjun Pan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

(2014) Xiaojiao Mu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Polarizable Force-Field for Cholesterol and Sphingomyelin

(2013) David Robinson   Journal of Chemical Theory and Computation

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

(2013) Lingle Wang et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Atomic-level simulation of current–voltage relationships in single-file ion channels

(2013) Morten Ø. Jensen et al.   JOURNAL OF GENERAL PHYSIOLOGY

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

Temperature Dependence of Gramicidin Channel Transport and Structure

(2013) Hyun Deok Song et al.   Journal of Physical Chemistry C

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

(2012) Jiajing Zhang et al.   Journal of Chemical Theory and Computation

The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field

(2012) Michael J. Schnieders et al.   Journal of Chemical Theory and Computation

Another Piece of the Membrane Puzzle: Extending Slipids Further

(2012) Joakim P. M. Jämbeck et al.   Journal of Chemical Theory and Computation

Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations

(2012) Yue Shi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automation of AMOEBA polarizable force field parameterization for small molecules

(2012) Johnny C. Wu et al.   THEORETICAL CHEMISTRY ACCOUNTS

Water permeation through DMPC lipid bilayers using polarizable charge equilibration force fields

(2011) Brad A. Bauer et al.   CHEMICAL PHYSICS LETTERS

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

(2011) Pengyu Ren et al.   Journal of Chemical Theory and Computation

A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A

(2011) Toni Giorgino et al.   Journal of Chemical Theory and Computation

Many-body exchange-repulsion in polarizable molecular mechanics. I. orbital-based approximations and applications to hydrated metal cation complexes

(2011) Robin Chaudret et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ion selectivity in channels and transporters

(2011) Benoît Roux et al.   JOURNAL OF GENERAL PHYSIOLOGY

Gramicidin A Backbone and Side Chain Dynamics Evaluated by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments. I: Molecular Dynamics Simulations

(2011) Helgi I. Ingólfsson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The ORCA program system

(2011) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

Electrostatics of Deformable Lipid Membranes

(2010) Igor Vorobyov et al.   BIOPHYSICAL JOURNAL

Multipole electrostatics in hydration free energy calculations

(2010) Yue Shi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

(2009) Dian Jiao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin

(2009) Shirley W. I. Siu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields

(2009) Sandeep Patel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The gramicidin channel ion permeation free-energy profile: Direct and indirect effects of CHARMM force field improvements

(2009) Morad Mustafa et al.   Interdisciplinary Sciences-Computational Life Sciences

Biomolecular simulations of membranes: Physical properties from different force fields

(2008) Shirley W. I. Siu et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes

(2008) Michael W. Forney et al.   PHYSICAL REVIEW E

Calculation of protein-ligand binding free energy by using a polarizable potential

(2008) D. Jiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics

(2008) G. De Fabritiis et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS