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Biomolecular simulations : methods and protocols / edited by Luca Monticelli, Emppu Salonen. — New York : Humana Press ; Springer, c2012. – (58.17/M592/v.924)

Contents

    Contents
    
    Preface
    Contributors
    PART I QUANTUM MECHANICS CALCULATIONS
    1 Ab Initio, Density Functional Theory, and Semi-Empirical Calculations
    2 Ab Initio Molecular Dynamics
    3 Introduction to QM/MM Simulations
    4 Computational Enzymology
    5 QM and QM/MM Simulations of Proteins
    PART II CLASSICAL MECHANICS: ATOMISTIC SIMULATIONS
    6 Classical Molecular Dynamics in a Nutshell
    7 Enhanced Sampling Algorithms 153
    8 Force Fields for Classical Molecular Dynamics
    9 Polarizable Force Fields
    10 Electrostatics Interactions in Classical Simulations 243
    11 An Introduction to Best Practices in Free Energy Calculations 271
    12 Recipes for Free Energy Calculations in Biomolecular Systems
    13 Molecular Docking Methodologies 339
    14 Simulation Studies of the Mechanism of Membrane Transporters 361
    15 Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It 407
    16 Simulations of Lipid Monolayers
    17 Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation
    18 Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water
    PART III MESOSCOPIC SIMULATIONS AND COARSE-GRAINED MODELS
    19 Systematic Methods for Structurally Consistent Coarse-Grained Models 487
    20 The Martini Coarse-Grained Force Field.
    21 Multiscale Molecular Modeling
    22 Coarse-Grained Models for Protein Folding and Aggregation
    23 Elastic Network Models: Theoretical and Empirical Foundations
    24 An Introduction to Dissipative Particle Dynamics
    25 Multiscale Molecular Dynamics Simulations of Membrane Proteins
    26 Vesicles and Vesicle Fusion: Coarse-Grained Simulations