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Biomolecular Simulations: Methods and Protocols

Handbook / Manual

Series: Methods in Molecular Biology Volume: 924

By: Luca Monticelli (Editor), Emppu Salonen (Editor)

715 pages, 41 colour & 20 b/w illustrations, 7 tables

Humana Press

Hardback | Sep 2012 | #201228 | ISBN-13: 9781627030168
Availability: Usually dispatched within 1-2 weeks Details
NHBS Price: £123.00 $150/€138 approx

About this book

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 modeling 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.


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. Andres 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 Rog
16. Simulations of Lipid Monolayers Svetlana Baoukina and D. Peter Tieleman
17. Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation Nicolas Foloppe , Marc Gueroult 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

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