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[资源] 生物分子模拟方法_英文原版

Biomolecular Simulation methods and protocols
PARTI QUANTUM MECHANICS CALCULATIONS
1 Ab Initio, Density Functional Theory, and Semi-Empirical Calculations . . . . . . . . . 3
2 Ab Initio Molecular Dynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3 Introduction to QM/MM Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4 Computational Enzymology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
5 QM and QM/MM Simulations of Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

PART II CLASSICAL MECHANICS: ATOMISTIC SIMULATIONS
6 Classical Molecular Dynamics in a Nutshell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
7 Enhanced Sampling Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
8 Force Fields for Classical Molecular Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
9 Polarizable Force Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
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. . . . . . . . . . . . . . . . . 313
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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431
17 Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation. . . . . . . 445
18 Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water . . . 469

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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533
21 Multiscale Molecular Modeling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 567
22 Coarse-Grained Models for Protein Folding and Aggregation . . . . . . . . . . . . . . . . . 585
23 Elastic Network Models: Theoretical and Empirical Foundations . . . . . . . . . . . . . . 601
24 An Introduction to Dissipative Particle Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . 617
25 Multiscale Molecular Dynamics Simulations of Membrane Proteins . . . . . . . . . . . . 635
26 Vesicles and Vesicle Fusion: Coarse-Grained Simulations. . . . . . . . . . . . . . . . . . . . . . 659

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