Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side-chain analogues

Effects of Lysine Substitution on Stability of Polyalanine α Helix

(2012) Sergei Y. Ponomarev et al.   Journal of Chemical Theory and Computation

The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers

(2012) Igor Vorobyov et al.   Journal of Chemical Theory and Computation

Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ

(2012) Timothy H. Click et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

(2012) Aude Marjolin et al.   THEORETICAL CHEMISTRY ACCOUNTS

Polarizable Simulations with Second-Order Interaction Model (POSSIM) Force Field: Developing Parameters for Alanine Peptides and Protein Backbone

(2011) Sergei Y. Ponomarev et al.   Journal of Chemical Theory and Computation

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

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

Molecular mechanisms of imidazole and benzene ring binding in proteins

(2009) A. V. Zhuravlev et al.   BIOCHEMISTRY-MOSCOW

Polarizable Simulations with Second-Order Interaction Model—Force Field and Software for Fast Polarizable Calculations: Parameters for Small Model Systems and Free Energy Calculations

(2009) George A. Kaminski et al.   Journal of Chemical Theory and Computation

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

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

Reproducing Basic pKaValues for Turkey Ovomucoid Third Domain Using a Polarizable Force Field

(2009) Timothy H. Click et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp20 in Thioredoxin

(2008) Changge Ji et al.   BIOPHYSICAL JOURNAL