Methods in Molecular Biology
Methods and Protocols
By: Emppu Salonen (Editor), Luca Monticelli (Editor)
Hardcover | 4 October 2012
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Hardcover
718 Pages
718 Pages
Dimensions(cm)
26.2 x 18.3 x 4.5
26.2 x 18.3 x 4.5
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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.
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 Part II: Classical Mechanics: Atomistic Simulations 5. QM and QM/MM Simulations of Proteins Thomas Steinbrecher and Marcus Elstner 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 & Anne Imberty Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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 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 Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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 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 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 Part II: Classical Mechanics: Atomistic Simulations 5. QM and QM/MM Simulations of Proteins Thomas Steinbrecher and Marcus Elstner 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 & Anne Imberty Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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 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 5. QM and QM/MM Simulations of Proteins Thomas Steinbrecher and Marcus Elstner 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 & Anne Imberty Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 Part III: Mesoscopic Simulations and Coarse-grained Models 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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 19. Systematic Methods for Structurally Consistent Coarse-grained Models W. G. Noidy 20. The Martini Coarse-Grained Force Field Siewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular Modeling Matej Praprotnik 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 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 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
ISBN: 9781627030168
ISBN-10: 1627030166
Series: Methods in Molecular Biology
Published: 4th October 2012
Format: Hardcover
Language: English
Number of Pages: 718
Audience: General Adult
Publisher: Springer Nature B.V.
Country of Publication: GB
Dimensions (cm): 26.2 x 18.3 x 4.5
Weight (kg): 1.36
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