Spis treści: Molecular Modeling of Proteins (Methods in Molecular Biology)


Preface, s. v
Contributors, s. ix

Part I Methodology

1. Molecular Dynamics Simulations, s. 3
Erik R. Lindahl
2. Monte Carlo Simulations, s. 25
David J. Earl and Michael W. Deem
3. Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes, s. 37
Jiali Gao, Dan T. Major, Yao Fan, Yen-lin Lin, Shuhua Ma, and Kin-Yiu Wong
4. Comparison of Protein Force Fields for Molecular Dynamics Simulations, s. 63
Olgun Guvench and Alexander D. MacKerell, Jr.
5. Normal Modes and Essential Dynamic, s. 89
Steven Hayward and Bert L. de Groot

Part II Free Energy Calculations

6. Calculation of Absolute Protein-Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method, s. 109
Hyung-June Woo
7. Free Energy Calculations Applied to Membrane Proteins, s. 121
Christophe Chipot

Part III Molecular Modeling of Membrane Proteins

8. Molecular Dynamics Simulations of Membrane Proteins, s. 147
Philip C. Biggin and Peter J. Bond
9. Membrane-Associated Proteins and Peptides, s. 161
Marc F. Lensink
10. Implicit Membrane Models for Membrane Protein Simulation, s. 181
Michael Feig

Part IV Protein Structure Determination

11. Comparative Modeling of Proteins, s. 199
Gerald H. Lushington
12. Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints, s. 213
Andrew J. Beevers and Andreas Kukol
13. Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes, s. 29
Gloria Fuentes, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin

Part V Conformational Change

14. Conformational Changes in Protein Function, s. 259
Haiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, and Yong Duan
15. Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations, s. 277
Hongxing Lei and Yong Duan
16. Modeling of Protein Misfolding in Disease, s. 297
Edyta B. Malolepsza

Part VI Applications to Drug Design

17. Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking, s. 333
David S. Wishart
18. Receptor Flexibility for Large-Scale In Silico Ligand Screens: Chances and Challenges, s. 353
B. Fischer, H. Merlitz, and W. Wenzel
19. Molecular Docking., s. 365
Garrett M. Morris and Marguerita Lim-Wilby
Index, s. 383

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