Vol. 13 No. 1 (2013)

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Published: 2013-01-05

Articles

Preface

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75 45
Poisson-Boltzmann Calculations: Van Der Waals or Molecular Surface?

Xiaodong Pang & Huan-Xiang Zhou

1-12

https://doi.org/10.4208/cicp.270711.140911s
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41120 4397
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

https://doi.org/10.4208/cicp.300611.120911s
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40928 4423
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

https://doi.org/10.4208/cicp.130911.121011s
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40840 4445
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

https://doi.org/10.4208/cicp.050711.111111s
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40745 4430
Modeling the Influence of Salt on the Hydrophobic Effect and Protein Fold Stability

Mihir S. Date & Brian N. Dominy

90-106

https://doi.org/10.4208/cicp.290711.121011s
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42454 6063
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

https://doi.org/10.4208/cicp.210711.111111s
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40963 4356
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

https://doi.org/10.4208/cicp.290711.180711s
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41161 4359
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

https://doi.org/10.4208/cicp.290711.181011s
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40745 4491
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

https://doi.org/10.4208/cicp.170811.211011s
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40842 4331
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

https://doi.org/10.4208/cicp.220711.041011s
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41006 4322
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

https://doi.org/10.4208/cicp.170911.131011s
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40538 4383
Examining Electrostatic Influences on Base-Flipping: A Comparison of TIP3P and GB Solvent Models

Allyn R. Brice & Brian N. Dominy

223-237

https://doi.org/10.4208/cicp.210711.121011s
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40631 4371
Structural Determinants of a Typical Leucine-Rich Repeat Protein

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

238-255

https://doi.org/10.4208/cicp.300711.230911s
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40728 4404
DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

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

256-268

https://doi.org/10.4208/cicp.170711.111111s
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40988 4362
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

https://doi.org/10.4208/cicp.300611.201011s
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41628 4651
Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation

Duan Chen & Guo-Wei Wei

285-324

https://doi.org/10.4208/cicp.050511.050811s
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40900 4346

Vol. 13 No. 1 (2013)

Articles

Preface

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

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

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

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

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

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

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

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

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

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

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

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

Structural Determinants of a Typical Leucine-Rich Repeat Protein

DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

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

Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation

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