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@article{Hornak2006
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@article{Izaguirre2010
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@article{Jorgensen1983
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@inbook{Kollman1997
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@article{Labute2008
   author = {Labute, Paul},
   title = {The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area},
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@article{Lamoureux2006
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@article{Lamoureux2003
   author = {Lamoureux, Guillaume and Roux, Benoit},
   title = {Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm},
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@article{Li2010
   author = {Li, D.W. and Br{\"u}schweiler, R.},
   title = {NMR-based protein potentials},
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@article{Lindorff-Larsen2010
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   title = {Improved side-chain torsion potentials for the Amber ff99SB protein force field},
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}

@article{Liu1989
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@article{Lopes2013,
    author = {Lopes, Pedro E. M. and Huang, Jing and Shim, Jihyun and Luo, Yun and Li, Hui and Roux, Benoît and MacKerell, Alexander D.},
    title = {Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator},
    journal = {Journal of Chemical Theory and Computation},
    volume = {9},
    number = {12},
    pages = {5430-5449},
    year = {2013},
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}

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@article{Mahoney2000
   author = {Mahoney, Michael W. and Jorgensen, William L.},
   title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
   journal = {Journal of Chemical Physics},
   volume = {112},
   pages = {8910-8922},
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@article{Markland2008
   author = {Markland, Thomas E. and Manolopoulos, David E.},
   title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations},
   journal = {Journal of Chemical Physics},
   volume = {129},
   number = {2},
   year = {2008},
   type = {Journal Article}
}

@article{Mongan2007
   author = {Mongan, John and Simmerling, Carlos and McCammon, J. Andrew and Case, David A. and Onufriev, Alexey},
   title = {Generalized Born model with a simple, robust molecular volume correction},
   journal = {Journal of Chemical Theory and Computation},
   volume = {3},
   number = {1},
   pages = {156-169},
   year = {2007},
   type = {Journal Article}
}

@article{Nguyen2013
   author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
   title = {Improved Generalized Born Solvent Model Parameters for Protein Simulations},
   journal = {Journal of Chemical Theory and Computation},
   volume = {9},
   number = {4},
   pages = {2020-2034},
   year = {2013},
   type = {Journal Article}
}

@article{Onufriev2004
   author = {Onufriev, Alexey and Bashford, Donald and Case, David A.},
   title = {Exploring protein native states and large-scale conformational changes with a modified generalized born model},
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   number = {22},
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@article{Parrinello1984
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   title = {Study of an F center in molten KCl},
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@misc{Ponder
   author = {Ponder, Jay W.},
   title = {Personal communication},
   type = {Personal Communication}
}

@article{Ren2002
   author = {Ren, P. and Ponder, Jay W.},
   title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations},
   journal = {Journal of Computational Chemistry},
   volume = {23},
   pages = {1497-1506},
   year = {2002},
   type = {Journal Article}
}

@article{Ren2003
   author = {Ren, P. and Ponder, Jay W.},
   title = {Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation},
   journal = {Journal of Physical Chemistry B},
   volume = {107},
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   year = {2003},
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@article{Schaefer1998
   author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin},
   title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model},
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@article{Schnieders2007
   author = {Schnieders, Michael J. and Ponder, Jay W.},
   title = {Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum},
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@article{Shirts2008
   author = {Shirts, Michael R. and Chodera, John D.},
   title = {Statistically optimal analysis of samples from multiple equilibrium states},
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@article{Shi2013
   author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
   title = {Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins},
   journal = {Journal of Chemical Theory and Computation},
   volume = {9},
   number = {9},
   pages = {4046-4063},
   year = {2013},
   type = {Journal Article}
}

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@article{Shirts2007
   author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
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   title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
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   journal = {Journal of Physical Chemistry B},
   volume = {111},
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@article{Shirts2005
   author = {Shirts, Michael R. and Pande, Vijay S.},
   title = {Solvation free energies of amino acid side chain analogs for common molecular mechanics water models},
   journal = {Journal of Chemical Physics},
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@article{Toukmaji1996
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@article{Wang2000
   author = {Wang, J. and Cieplak, P. and Kollman, P.A.},
   title = {How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?},
   journal = {Journal of Computational Chemistry},
   volume = {21},
   pages = {1049-1074},
   year = {2000},
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@article{Wang2014
   author = {Wang, Lee-Ping and Martinez, Todd J. and Pande, Vijay S.},
   title = {Building force fields: an automatic, systematic, and reproducible approach},
   journal = {Journal of Physical Chemistry Letters},
   volume = {5},
   pages = {1885-1891},
   year = {2014},
   type = {Journal Article}
}