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The Resource Biomolecular simulations : methods and protocols, edited by Luca Monticelli, Emppu Salonen, (electronic book)

Biomolecular simulations : methods and protocols, edited by Luca Monticelli, Emppu Salonen, (electronic book)

Label
Biomolecular simulations : methods and protocols
Title
Biomolecular simulations
Title remainder
methods and protocols
Statement of responsibility
edited by Luca Monticelli, Emppu Salonen
Contributor
Editor
Subject
Language
eng
Summary
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
Member of
Cataloging source
SCB
Dewey number
570.285
Illustrations
illustrations
Index
index present
LC call number
QP517.M65
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
http://library.link/vocab/relatedWorkOrContributorName
  • Monticelli, Luca
  • Salonen, Emppu
Series statement
Methods in molecular biology,
Series volume
v. 924
http://library.link/vocab/subjectName
  • Molecular dynamics
  • Biomolecules
  • Molecular biology
  • Molecular biology
  • Molecular Dynamics Simulation
  • Models, Molecular
  • Computer Simulation
Label
Biomolecular simulations : methods and protocols, edited by Luca Monticelli, Emppu Salonen, (electronic book)
Instantiates
Publication
Bibliography note
Includes bibliographical references and index
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
Contents
  • QM and QM/MM simulations of proteins
  • Thomas Steinbrecher and Marcus Elstner
  • Classical molecular dynamics in a nutshell
  • Susanna Hug
  • Enhanced sampling algorithms
  • Ayori Mitsutake, Yoshiharu Mori, and Yuko Okamoto
  • Force fields for classical molecular dynamics
  • Luca Monticelli and D. Peter Tieleman
  • Polarizable force fields
  • Hanne S. Antila and Emppu Salonen
  • Ab Initio, density functional theory, and semi-empirical calculations
  • Electrostatics interactions in classical simulations
  • G. Andres Cisneros, Volodymyr Babin, and Celeste Sagui
  • Introduction to best practices in free energy calculations
  • Michael R. Shirts and David L. Mobley
  • Recipes for free energy calculations in biomolecular systems
  • Mahmoud Moradi [and others]
  • Molecular docking methodologies
  • Andrea Bortolato [and others]
  • Simulation studies of the mechanism of membrane transporters
  • Giray Enkavi [and others]
  • Mikael P. Johansson, Ville R.I. Kaila, and Dage Sundholm
  • Molecular dynamics simulations of lipid bilayers : simple recipe of how to do it
  • Hector Martinez-Seara and Tomasz Rog
  • Simulations of lipid monolayers
  • Svetlana Baoukina and D. Peter Tieleman
  • Simulating DNA by molecular dynamics : aims, methods, and validation
  • Nicolas Foloppe, Marc Gueroult, and Brigitte Hartmann
  • Simulation of carbohydrates, from molecular docking to dynamics in water
  • Nicolas Sapay, Alessandra Nurisso, and Anne Imberty
  • Systematic methods for structurally consistent coarse-grained models
  • W.G. Noid
  • Ab Initio molecular dynamics
  • Martini coarse-grained force field
  • Xavier Periole and Siewert-Jan Marrink
  • Multiscale molecular modeling
  • Matej Praprotnik and Luigi Delle Site
  • Coarse-grained models for protein folding and aggregation
  • Philippe Derreumaux
  • Elastic network models : theoretical and empirical foundations
  • Yves-Henri Sanejouand
  • Introduction to dissipative particle dynamics
  • Zhong-Yuan Lu and Yong-Lei Wang
  • Kari Laasonen
  • Multiscale molecular dynamics simulations of membrane proteins
  • Syma Khalid and Peter J. Bond
  • Vesicles and vesicle fusion : coarse-grained simulations
  • Julian C. Shillcock
  • Introduction to QM/MM simulations
  • Gerrit Groenhof
  • Computational enzymology
  • Alessio Lodola and Adrian J. Mulholland
Control code
SPR815525191
Extent
1 online resource (xiii, 702 pages)
Form of item
online
Isbn
9781627030168
Media category
computer
Media MARC source
rdamedia
Media type code
  • c
Other physical details
illustrations (some color).
Reproduction note
Electronic resource.
Specific material designation
remote
Label
Biomolecular simulations : methods and protocols, edited by Luca Monticelli, Emppu Salonen, (electronic book)
Publication
Bibliography note
Includes bibliographical references and index
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
Contents
  • QM and QM/MM simulations of proteins
  • Thomas Steinbrecher and Marcus Elstner
  • Classical molecular dynamics in a nutshell
  • Susanna Hug
  • Enhanced sampling algorithms
  • Ayori Mitsutake, Yoshiharu Mori, and Yuko Okamoto
  • Force fields for classical molecular dynamics
  • Luca Monticelli and D. Peter Tieleman
  • Polarizable force fields
  • Hanne S. Antila and Emppu Salonen
  • Ab Initio, density functional theory, and semi-empirical calculations
  • Electrostatics interactions in classical simulations
  • G. Andres Cisneros, Volodymyr Babin, and Celeste Sagui
  • Introduction to best practices in free energy calculations
  • Michael R. Shirts and David L. Mobley
  • Recipes for free energy calculations in biomolecular systems
  • Mahmoud Moradi [and others]
  • Molecular docking methodologies
  • Andrea Bortolato [and others]
  • Simulation studies of the mechanism of membrane transporters
  • Giray Enkavi [and others]
  • Mikael P. Johansson, Ville R.I. Kaila, and Dage Sundholm
  • Molecular dynamics simulations of lipid bilayers : simple recipe of how to do it
  • Hector Martinez-Seara and Tomasz Rog
  • Simulations of lipid monolayers
  • Svetlana Baoukina and D. Peter Tieleman
  • Simulating DNA by molecular dynamics : aims, methods, and validation
  • Nicolas Foloppe, Marc Gueroult, and Brigitte Hartmann
  • Simulation of carbohydrates, from molecular docking to dynamics in water
  • Nicolas Sapay, Alessandra Nurisso, and Anne Imberty
  • Systematic methods for structurally consistent coarse-grained models
  • W.G. Noid
  • Ab Initio molecular dynamics
  • Martini coarse-grained force field
  • Xavier Periole and Siewert-Jan Marrink
  • Multiscale molecular modeling
  • Matej Praprotnik and Luigi Delle Site
  • Coarse-grained models for protein folding and aggregation
  • Philippe Derreumaux
  • Elastic network models : theoretical and empirical foundations
  • Yves-Henri Sanejouand
  • Introduction to dissipative particle dynamics
  • Zhong-Yuan Lu and Yong-Lei Wang
  • Kari Laasonen
  • Multiscale molecular dynamics simulations of membrane proteins
  • Syma Khalid and Peter J. Bond
  • Vesicles and vesicle fusion : coarse-grained simulations
  • Julian C. Shillcock
  • Introduction to QM/MM simulations
  • Gerrit Groenhof
  • Computational enzymology
  • Alessio Lodola and Adrian J. Mulholland
Control code
SPR815525191
Extent
1 online resource (xiii, 702 pages)
Form of item
online
Isbn
9781627030168
Media category
computer
Media MARC source
rdamedia
Media type code
  • c
Other physical details
illustrations (some color).
Reproduction note
Electronic resource.
Specific material designation
remote

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