Articles

• Preface

  i-v

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

  Xiaodong Pang & Huan-Xiang Zhou

  1-12

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

  Lin Wang, Zhe Zhang, Walter Rocchia & Emil Alexov

  13-30

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

  Fang Zheng & Chang-Guo Zhan

  31-60

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

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

  61-89

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

  Mihir S. Date & Brian N. Dominy

  90-106

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• 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

  107-128

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• 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

  129-149

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

  Mohammad Mirzadeh, Maxime Theillard, Asdís Helgadóttir, David Boy & Frédéric Gibou

  150-173

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

  Dexuan Xie & Hans W. Volkmer

  174-194

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• 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

  195-206

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• 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

  207-222

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

  Allyn R. Brice & Brian N. Dominy

  223-237

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• Structural Determinants of a Typical Leucine-Rich Repeat Protein

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

  238-255

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• DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

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

  256-268

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• 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

  269-284

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

  Duan Chen & Guo-Wei Wei

  285-324

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