Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics.
This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.
Author(s): Harold A. Scheraga (auth.), Adam Liwo (eds.)
Series: Springer Series in Bio-/Neuroinformatics 1
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2014
Language: English
Pages: 810
Tags: Computational Intelligence;Computational Biology/Bioinformatics;Protein Science;Theoretical and Computational Chemistry;Mechanics
Front Matter....Pages 1-12
Simulations of the Folding of Proteins: A Historical Perspective....Pages 1-23
Coarse-Grained Protein Models in Structure Prediction....Pages 25-53
Coarse-Grained Modeling of Protein Dynamics....Pages 55-79
Physics-Based Modeling of Side Chain - Side Chain Interactions in the UNRES Force Field....Pages 81-107
Modeling Nucleic Acids at the Residue-Level Resolution....Pages 109-149
Modeling of Electrostatic Effects in Macromolecules....Pages 151-193
Optimizations of Protein Force Fields....Pages 195-247
Enhanced Sampling for Biomolecular Simulations....Pages 249-267
Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments....Pages 269-293
Mechanostability of Virus Capsids and Their Proteins in Structure-Based Models....Pages 295-315
Computer Modelling of the Lipid Matrix of Biomembranes....Pages 317-355
Modeling of Membrane Proteins....Pages 357-431
All-Atom Monte Carlo Simulations of Protein Folding and Aggregation....Pages 433-444
Molecular Dynamics Studies on Amyloidogenic Proteins....Pages 445-481
Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis....Pages 483-524
Bioinformatical Approaches to Unstructured/Disordered Proteins and Their Interactions....Pages 525-556
Theoretical and Computational Aspects of Protein Structural Alignment....Pages 557-598
Simulation of the Protein Folding Process....Pages 599-638
13 C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information....Pages 639-683
When Water Plays an Active Role in Electronic Structure: Insights from First-Principles Molecular Dynamics Simulations of Biological Systems....Pages 685-710
Electronic Properties of Iron Sites and Their Active Forms in Porphyrin-Type Architectures....Pages 711-782
Bioinorganic Reaction Mechanisms – Quantum Chemistry Approach....Pages 783-808
Back Matter....Pages 809-810
