Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

From Bioinformatics to Molecular Quantum Mechanics

Editors:

ISBN: 978-3-642-28553-0 (Print) 978-3-642-28554-7 (Online)

Table of contents (22 chapters)

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  1. Front Matter

    Pages 1-12

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    Chapter

    Pages 1-23

    Simulations of the Folding of Proteins: A Historical Perspective

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    Chapter

    Pages 25-53

    Coarse-Grained Protein Models in Structure Prediction

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    Chapter

    Pages 55-79

    Coarse-Grained Modeling of Protein Dynamics

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    Chapter

    Pages 81-107

    Physics-Based Modeling of Side Chain - Side Chain Interactions in the UNRES Force Field

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    Chapter

    Pages 109-149

    Modeling Nucleic Acids at the Residue-Level Resolution

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    Chapter

    Pages 151-193

    Modeling of Electrostatic Effects in Macromolecules

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    Chapter

    Pages 195-247

    Optimizations of Protein Force Fields

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    Chapter

    Pages 249-267

    Enhanced Sampling for Biomolecular Simulations

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    Chapter

    Pages 269-293

    Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments

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    Chapter

    Pages 295-315

    Mechanostability of Virus Capsids and Their Proteins in Structure-Based Models

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    Chapter

    Pages 317-355

    Computer Modelling of the Lipid Matrix of Biomembranes

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    Chapter

    Pages 357-431

    Modeling of Membrane Proteins

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    Chapter

    Pages 433-444

    All-Atom Monte Carlo Simulations of Protein Folding and Aggregation

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    Chapter

    Pages 445-481

    Molecular Dynamics Studies on Amyloidogenic Proteins

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    Chapter

    Pages 483-524

    Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis

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    Chapter

    Pages 525-556

    Bioinformatical Approaches to Unstructured/Disordered Proteins and Their Interactions

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    Chapter

    Pages 557-598

    Theoretical and Computational Aspects of Protein Structural Alignment

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    Chapter

    Pages 599-638

    Simulation of the Protein Folding Process

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    Chapter

    Pages 639-683

    13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information

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    Chapter

    Pages 685-710

    When Water Plays an Active Role in Electronic Structure: Insights from First-Principles Molecular Dynamics Simulations of Biological Systems

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