Molecular modeling of proteins

著者

    • Kukol, Andreas

書誌事項

Molecular modeling of proteins

edited by Andreas Kukol

（Methods in molecular biology / John M. Walker, series editor, 1215）

Humana Press, c2015

2nd ed.

大学図書館所蔵 件 / 全2件

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注記

Includes bibliographical references and index

内容説明・目次

内容説明

Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.

目次

Part I: Simulation Methods 1. Molecular Dynamics Simulations Erik Lindahl 2. Transition Path Sampling with Quantum/Classical Mechanics for Reaction Rates Frauke Grater and Wenjin Li 3. Current Status of Protein Force Fields for Molecular Dynamics Simulations Pedro E.M. Lopes, Olgun Guvench, and Alexander D. MacKerell, Jr. 4. Lipid Membranes for Membrane Proteins Andreas Kukol 5. Molecular Dynamics Simulations of Membrane Proteins Philip C. Biggin and Peter J. Bond 6. Membrane-Associated Proteins and Peptides Marc F. Lensink 7. Coarse-Grained Force Fields for Molecular Simulations Jonathan Barnoud and Luca Monticelli 8. Tackling Sampling Challenges in Biomolecular Simulations Alessandro Barducci, Jim Pfaendtner, and Massimiliano Bonomi 9. Calculation of Binding Free Energies Vytautas Gapsys, Servaas Michielssens, Jan-Henning Peters, Bert L. de Groot, and Hadas Leonov Part II: Conformational Change 10. The Use of Experimental Structures to Model Protein Dynamics Ataur R. Katebi, Kannan Sankar, Kejue Jia, and Robert L. Jernigan 11. Computing Ensembles of Transitions with Molecular Dynamics Simulations Juan Perilla and Thomas B. Woolf 12. Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter Patrick C. Gedeon, James R. Thomas, and Jeffry D. Madura 13. Simulations and Experiments in Protein Folding Giovanni Settanni Part III: Protein Structure Determination 14. Comparative Modeling of Proteins Gerald H. Lushington 15. De Novo Membrane Protein Structure Prediction Timothy Nugent 16. NMR-Based Modeling and Refinement of Protein 3D Structures Wim F. Vranken, Geerten W. Vuister, and Alexandre M.J.J. Bonvin Part IV: Protein-Ligand Interactions 17. Methods for Predicting Protein Ligand Binding Sites Zhong-Ru Xie and Ming-Jing Hwang 18. Information-Driven Structural Modelling of Protein-Protein Interactions Joao P.G.L.M. Rodrigues, Ezgi Karaca, and Alexandre M.J.J. Bonvin 19. Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking David S. Wishart 20. Molecular Docking to Flexible Targets Jesper Sorensen, OEzlem Demir, Robert V. Swift, Victoria A. Feher, and Rommie E. Amaro

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