Molecular modeling of proteins
Author(s)
Bibliographic Information
Molecular modeling of proteins
（Methods in molecular biology / John M. Walker, series editor, 1215）
Humana Press, c2015
2nd ed.
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
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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