فهرست مطالب کتاب روش های محاسباتی برای مطالعه ساختار و دینامیک مولکولهای زیستی و فرایندهای زیست مولکولی از بیوانفورماتیک تا مکانیک کوانتوم مولکولی:

Part I Introduction

Simulations of the Folding of Proteins: A Historical Perspective . . . . . . 3

Part II Molecular Simulations: Methodology

Protein Structure Prediction Using Coarse-Grained Models . . . . . . . . . 27

Protein Dynamics Simulations Using Coarse-Grained Models . . . . . . . . 61

Physics-Based Modeling of Side Chain—Side Chain Interactions in the UNRES Force Field . . . . . . . . . 89

Modeling Nucleic Acids at the Residue–Level Resolution . . . . . . . . . . . . 117

Modeling of Electrostatic Effects in Macromolecules . . . . . . . . . . . . . . . 163

Optimizations of Protein Force Fields . . . . . . . . . . . . . . . . . . . . . . . . . . 203

Enhanced Sampling for Biomolecular Simulations . . . . . . . . . . . . . . . . . 257

Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments .. . . 281

Part III Molecular Simulations: Applications

Mechanostability of Virus Capsids and Their Proteins in Structure-Based Coarse-Grained Models . . 307

Computer Modelling of the Lipid Matrix of Biomembranes . . . . . . . . . 331

Modeling of Membrane Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371

Peptide Folding in Cellular Environments: A Monte Carlo and Markov Modeling Approach . . .. . . . 453

Molecular Dynamics Studies on Amyloidogenic Proteins . . . . . . . . . . . . 467

Raman and Infrared Spectra of Acoustical, Functional Modes of Proteins from All-Atom and Coarse-Grained Normal Mode Analysis . . . . .. . 501

Explicit-Solvent All-Atom Molecular Dynamics of Peptide Aggregation . . .  . . . . . . . . . . 541

Part IV Use of Structural Database or Experimental Information in Modeling Protein Structure and Dynamics

Bioinformatical Approaches to Unstructured/Disordered Proteins and Their Complexes . . . . . . . 561

Theoretical and Computational Aspects of Protein Structural Alignment . . . . . . . . . . . 597

Fuzzy Oil Drop Model Application—From Globular Proteins to Amyloids . . . . . . . . . . . 639

13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information . . . . .  . . . . . 659

Protein Secondary Structure Assignments and Their Usefulness for Dihedral Angle Prediction . . .  . . 699

Part V Applications of Molecular Quantum Mechanics

When Water Plays an Active Role in Electronic Structure. Insights from First-Principles Molecular Dynamics Simulations of Biological Systems . . . . . . . . 715

Electronic Properties of Iron Sites and Their Active Forms in Porphyrin-Type Architectures . . . . .  . 755

Bioinorganic Reaction Mechanisms—Quantum Chemistry Approach . . . . . . .. . . . . . . 825

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851

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