Biomolecular Simulations: Methods and Protocols

ISBN-13: 9781627030168 / Angielski / Twarda / 2012 / 702 str.

Luca Monticelli; Emppu Salonen

Opis

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.

Spis treści

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