Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics ... Series on Bio- and Neurosystems Book 8)

This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research. Front Matter ....Pages i-xv Front Matter ....Pages 1-1 Simulations of the Folding of Proteins: A Historical Perspective (Harold A. Scheraga)....Pages 3-24 Front Matter ....Pages 25-25 Protein Structure Prediction Using Coarse-Grained Models (Maciej Blaszczyk, Dominik Gront, Sebastian Kmiecik, Mateusz Kurcinski, Michal Kolinski, Maciej Pawel Ciemny et al.)....Pages 27-59 Protein Dynamics Simulations Using Coarse-Grained Models (Sebastian Kmiecik, Jacek Wabik, Michal Kolinski, Maksim Kouza, Andrzej Kolinski)....Pages 61-87 Physics-Based Modeling of Side Chain—Side Chain Interactions in the UNRES Force Field (Mariusz Makowski)....Pages 89-115 Modeling Nucleic Acids at the Residue–Level Resolution (Filip Leonarski, Joanna Trylska)....Pages 117-161 Modeling of Electrostatic Effects in Macromolecules (Yury N. Vorobjev)....Pages 163-202 Optimizations of Protein Force Fields (Yoshitake Sakae, Yuko Okamoto)....Pages 203-256 Enhanced Sampling for Biomolecular Simulations (Workalemahu Berhanu, Ping Jiang, Ulrich H. E. Hansmann)....Pages 257-280 Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments (Alfredo E. Cardenas)....Pages 281-303 Front Matter ....Pages 305-305 Mechanostability of Virus Capsids and Their Proteins in Structure-Based Coarse-Grained Models (Marek Cieplak)....Pages 307-330 Computer Modelling of the Lipid Matrix of Biomembranes (Marta Pasenkiewicz-Gierula, Michał Markiewicz)....Pages 331-370 Modeling of Membrane Proteins (Dorota Latek, Bartosz Trzaskowski, Szymon Niewieczerzał, Przemysław Miszta, Krzysztof Młynarczyk, Aleksander Dębiński et al.)....Pages 371-451 Peptide Folding in Cellular Environments: A Monte Carlo and Markov Modeling Approach (Daniel Nilsson, Sandipan Mohanty, Anders Irbäck)....Pages 453-466 Molecular Dynamics Studies on Amyloidogenic Proteins (Sylwia Rodziewicz-Motowidło, Emilia Sikorska, Justyna Iwaszkiewicz)....Pages 467-499 Raman and Infrared Spectra of Acoustical, Functional Modes of Proteins from All-Atom and Coarse-Grained Normal Mode Analysis (Adrien Nicolaï, Patrice Delarue, Patrick Senet)....Pages 501-539 Explicit-Solvent All-Atom Molecular Dynamics of Peptide Aggregation (Maksim Kouza, Andrzej Kolinski, Irina Alexandra Buhimschi, Andrzej Kloczkowski)....Pages 541-558 Front Matter ....Pages 559-559 Bioinformatical Approaches to Unstructured/Disordered Proteins and Their Complexes (Bálint Mészáros, Zsuzsanna Dosztányi, Erzsébet Fichó, Csaba Magyar, István Simon)....Pages 561-596 Theoretical and Computational Aspects of Protein Structural Alignment (Paweł Daniluk, Bogdan Lesyng)....Pages 597-637 Fuzzy Oil Drop Model Application—From Globular Proteins to Amyloids (M. Banach, L. Konieczny, I. Roterman)....Pages 639-658 13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information (Jorge A. Vila, Yelena A. Arnautova)....Pages 659-698 Protein Secondary Structure Assignments and Their Usefulness for Dihedral Angle Prediction (Eshel Faraggi, Andrzej Kloczkowski)....Pages 699-712 Front Matter ....Pages 713-713 When Water Plays an Active Role in Electronic Structure. Insights from First-Principles Molecular Dynamics Simulations of Biological Systems (Giovanni La Penna, Oliviero Andreussi)....Pages 715-753 Electronic Properties of Iron Sites and Their Active Forms in Porphyrin-Type Architectures (Mariusz Radoń, Ewa Broclawik)....Pages 755-823 Bioinorganic Reaction Mechanisms—Quantum Chemistry Approach (Tomasz Borowski, Ewa Broclawik)....Pages 825-849 Back Matter ....Pages 851-851