Introduction to best practices in free energy calculations / Michael R. Shirts and David L. Mobley -- 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 -- Multiscale molecular modeling / Matej Praprotnik and Luigi Delle Site -- Molecular docking methodologies / Andrea Bortolato ... [et al.] -- Simulation studies of the mechanism of membrane transporters / Giray Enkavi ... [et al.] -- 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 -- Vesicles and vesicle fusion : coarse-grained simulations / Julian C. Shillcock. 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.
Series:
Methods in molecular biology, 1064-3745 ; 924 Springer protocols
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