Computational Electrostatics for Biological Applications: Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules

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Walter Rocchia, Michela Spagnuolo
Springer, Nov 29, 2014 - Science - 306 pages

This book presents established and new approaches to perform calculations of electrostatic interactions at the nanoscale, with particular focus on molecular biology applications. It is based on the proceedings of the Computational Electrostatics for Biological Applications international meeting, which brought together researchers in computational disciplines to discuss and explore diverse methods to improve electrostatic calculations. Fostering an interdisciplinary approach to the description of complex physical and biological problems, this book encompasses contributions originating in the fields of geometry processing, shape modeling, applied mathematics, and computational biology and chemistry. The main topics covered are theoretical and numerical aspects of the solution of the Poisson-Boltzmann equation, surveys and comparison among geometric approaches to the modelling of molecular surfaces and related discretization and computational issues. It also includes a number of contributions addressing applications in biology, biophysics and nanotechnology. The book is primarily intended as a reference for researchers in the computational molecular biology and chemistry fields. As such, it also aims at becoming a key source of information for a wide range of scientists who need to know how modeling and computing at the molecular level may influence the design and interpretation of their experiments.

 

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Contents

1 Electrostatics Models for Biology
1
2 Classical Density Functional Theory of Ionic Solutions
17
3 A Comprehensive Exploration of Physical and Numerical Parameters in the PoissonBoltzmann Equation for Applications to ReceptorLigand Bin...
39
Energy and Surface Electrostatic Properties
73
5 Efficient and Stable Method to Solve PoissonBoltzmann Equation with Steep Gradients
111
Progress Challenges and Important Lessons from CEBA 2013
121
7 The Accuracy of Generalized Born Forces
143
8 StateoftheArt and Perspectives of Geometric and Implicit Modeling for Molecular Surfaces
156
9 Triangulating GaussianLike Surfaces of Molecules with Millions of Atoms
177
A Tutorial on NanoShaper
199
11 The Representation of Electrostatics for Biological Molecules
215
12 Using Structural and PhysicalChemical Parameters to Identify Classify and Predict Functional Districts in ProteinsThe Role of Electrostatic Potential
226
The Case Study of Myoglobin
255
14 SelfInclusion Complexes of Monofunctionalized BetaCyclodextrins as HostGuest Interaction Model Systems and Simple and Sensitive Testbeds fo...
271
15 Modeling ProteinLigand Interaction with Finite Absorbing Markov Chain
297
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