Title Biomolecular simulations : methods and protocols / edited by Luca Monticelli, Emppu Salonen

Published New York : Humana Press : Springer, ©2013

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Description 1 online resource (xiii, 702 pages) : illustrations (some color) Series Methods in molecular biology, 1940-6029 ; v. 924 Methods in molecular biology (Clifton, N.J.) ; volume 924. 1064-3745 Contents Ab Initio, density functional theory, and semi-empirical calculations / Mikael P. Johansson, Ville R.I. Kaila, and Dage Sundholm -- Ab Initio molecular dynamics / Kari Laasonen -- Introduction to QM/MM simulations / Gerrit Groenhof -- Computational enzymology / Alessio Lodola and Adrian J. Mulholland -- 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 -- 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] -- 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 -- 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 -- Multiscale molecular dynamics simulations of membrane proteins / Syma Khalid and Peter J. Bond -- Vesicles and vesicle fusion : coarse-grained simulations / Julian C. Shillcock 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 Analysis moleculen molecules bioinformatics computertechnieken computer techniques simulatie simulation Molecular Biology (General) Moleculaire biologie (algemeen) Bibliography Includes bibliographical references and index Notes English Print version record Subject Molecular dynamics -- Mathematical models Biomolecules -- Mathematical models Molecular biology -- Research. Molecular biology -- Computer simulation Digital computer simulation. Computer simulation. Molecular Dynamics Simulation Models, Molecular Computer Simulation simulation. Digital computer simulation Computer simulation Biomolecules -- Mathematical models Molecular biology -- Computer simulation Molecular biology -- Research Molecular dynamics -- Mathematical models Genre/Form Laboratory manuals Laboratory manuals. Manuels de laboratoire. Form Electronic book Author Monticelli, Luca. Salonen, Emppu. ISBN 9781627030175 1627030174

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