Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics

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