Articles

• Preface

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  210 147 Pages:i-v

• Poisson-Boltzmann Calculations: Van Der Waals or Molecular Surface?

  Xiaodong Pang, Huan-Xiang Zhou

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  41282 4492 Pages:1-12

• Using DelPhi Capabilities to Mimic Protein's Conformational Reorganization with Amino Acid Specific Dielectric Constants

  Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

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  41068 4533 Pages:13-30

• Computational Modeling of Solvent Effects on Protein-Ligand Interactions Using Fully Polarizable Continuum Model and Rational Drug Design

  Fang Zheng, Chang-Guo Zhan

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  40994 4559 Pages:31-60

• Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution

  Sergio Decherchi, Jose Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

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  40906 4540 Pages:61-89

• Modeling the Influence of Salt on the Hydrophobic Effect and Protein Fold Stability

  Mihir S. Date, Brian N. Dominy

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  42668 6187 Pages:90-106

• Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver

  Bo Zhang, Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun, J. Andrew McCammon

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  41131 4477 Pages:107-128

• Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model

  Wei Song, Yuchun Lin, Andrij Baumketner, Shaozhong Deng, Wei Cai, Donald J. Jacobs

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  41312 4487 Pages:129-149

• An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations

  Mohammad Mirzadeh, Maxime Theillard, Asdis Helgadottir, David Boy, Frederic Gibou

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  40916 4592 Pages:150-173

• A Modified Nonlocal Continuum Electrostatic Model for Protein in Water and Its Analytical Solutions for Ionic Born Models

  Dexuan Xie, Hans W. Volkmer

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  40979 4421 Pages:174-194

• Numerical Optimization of a Walk-on-Spheres Solver for the Linear Poisson-Boltzmann Equation

  Travis Mackoy, Robert C. Harris, Jesse Johnson, Michael Mascagni, Marcia O. Fenley

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  41141 4422 Pages:195-206

• In Silico Investigation of pH-Dependence of Prolactin and Human Growth Hormone Binding to Human Prolactin Receptor

  Lin Wang, Shawn Witham, Zhe Zhang, Lin Li, Michael Hodsdon, Emil Alexov

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  40674 4483 Pages:207-222

• Examining Electrostatic Influences on Base-Flipping: A Comparison of TIP3P and GB Solvent Models

  Allyn R. Brice, Brian N. Dominy

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  40781 4483 Pages:223-237

• Structural Determinants of a Typical Leucine-Rich Repeat Protein

  Joao M. Martins, Rui M. Ramos, Irina S. Moreira

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  40872 4506 Pages:238-255

• DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

  Lane W. Votapka, Luke Czapla, Maxim Zhenirovskyy, Rommie E. Amaro

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  41119 4499 Pages:256-268

• DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes

  Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia, Emil Alexov

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  41794 4792 Pages:269-284

• Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation

  Duan Chen, Guo-Wei Wei

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  41036 4473 Pages:285-324