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

✍ Scribed by Adam Liwo

Publisher: Springer International Publishing
Year: 2019
Tongue: English
Leaves: 849
Series: Springer Series on Bio- and Neurosystems 8
Edition: 2nd ed.
Category: Library

No coin nor oath required. For personal study only.

✦ Synopsis

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.

✦ Table of Contents

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

✦ Subjects

Engineering; Computational Intelligence; Computational Biology/Bioinformatics; Protein Science; Theoretical and Computational Chemistry; Statistical Physics and Dynamical Systems

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