Biomolecular Simulations

Methods and Protocols
2013
ISBN: 978-1-62703-016-8
Verlag: Humana Press

Buch, Englisch, Band 924, 702 Seiten, Format (B × H): 183 mm x 260 mm, Gewicht: 14707 g

Reihe: Methods in Molecular Biology

Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced.

Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.

Zielgruppe

Professional/practitioner

Autoren/Hrsg.

Salonen, Emppu

Monticelli, Luca

Fachgebiete

• Mathematik | Informatik EDV | Informatik Angewandte Informatik Bioinformatik
• Naturwissenschaften Biowissenschaften Angewandte Biologie Bioinformatik
• Naturwissenschaften Biowissenschaften Kohlenhydrate
• Naturwissenschaften Biowissenschaften Lipidologie
• Naturwissenschaften Biowissenschaften Proteinforschung
• Naturwissenschaften Biowissenschaften Molekularbiologie

Inhaltsverzeichnis

Part I: Quantum Mechanics Calculations
1. Ab initio, Density Functional Theory, and Semi-empirical Calculations
Mikael P. Johansson, Ville R. I. Kaila and Dage Sundholm
 
2. Ab initio Molecular Dynamics
Kari Laasonen
 
3. Introduction to QM/MM simulations
Gerrit Groenhof
 
4. Computational Enzymology
Alessio Lodola and Adrian J. Mulholland
 
5. QM and QM/MM Simulations of Proteins
Thomas Steinbrecher and Marcus Elstner
 
Part II: Classical Mechanics: Atomistic Simulations 
 
6. Classical Molecular Dynamics in a Nutshell
Susanna Hug
 
7. Enhanced Sampling Algorithms
Ayori Mitsutake, Yoshiharu Mori, and Yuko Okamoto
 
8. Force Fields for Classical Molecular Dynamics
Luca Monticelli  and D. Peter Tieleman
 
9. Polarizable Force Fields
Hanne S. Antila and Emppu Salonen
 
10. Electrostatics interactions in classical simulations
G. Andrés Cisneros, Volodymyr Babin, and Celeste Sagui
 
11. An Introduction to Best Practices in Free Energy
Calculations
Michael R. Shirts  and David L. Mobley
 
12. Recipes for Free Energy Calculations in Biomolecular Systems
Mahmoud Moradi, Volodymyr Babin, Celeste Sagui, and Christopher Roland
 
13. Molecular Docking Methodologies
Andrea Bortolato, Marco Fanton, Jonathan S. Mason and Stefano Moro
 
14. Simulation Studies of the Mechanism of Membrane Transporters
Giray Enkavi, Jing Li, Paween Mahinthichaichan, Po-Chao Wen, Zhijian Huang, Saher A. Shaikh and Emad Tajkhorshid
 
15. Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It
Hector Martinez-Seara and Tomasz Róg
 
16. Simulations of Lipid Monolayers
Svetlana Baoukina and D. Peter Tieleman
 
17. Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation
Nicolas Foloppe, Marc Guéroult and Brigitte Hartmann
 
18. Simulation of Carbohydrates, From Molecular Docking to Dynamics in Water
Nicolas Sapay, Alessandra Nurisso and Anne Imberty  
 
Part III: Mesoscopic Simulations and Coarse-grained Models
 
19. Systematic Methods for Structurally Consistent Coarse-grained
Models
W. G. Noid
 
20. The Martini Coarse-Grained Force Field
Siewert-Jan Marrink & Xavier Periole
 
21. Multiscale Molecular Modeling
Matej Praprotnik and Luigi Delle Site
 
22. Coarse-grained Models for Protein Folding and Aggregation
Philippe Derreumaux 
23. Elastic Network Models: Theoretical and Empirical Foundations
Yves-Henri Sanejouand
 
24. An Introduction to Dissipative Particle Dynamics
Zhong-Yuan Lu, Yong-Lei Wang
 
25. Multiscale Molecular Dynamics Simulations of Membrane Proteins
Syma Khalid  and Peter J Bond
 
26. Vesicles and Vesicle Fusion: Coarse-grained Simulations
Julian C Shillcock