Molecular Modeling of Proteins (2^nd Ed., 2nd ed. 2015)
Methods in Molecular Biology Series, Vol. 1215

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.

Part I: Simulation Methods

1. Molecular Dynamics Simulations

            Erik Lindahl

2. Transition Path Sampling with Quantum/Classical Mechanics for Reaction Rates

            Frauke Gräter 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

            João 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 Sørensen, Özlem Demir, Robert V. Swift, Victoria A. Feher, and Rommie E. Amaro

Includes cutting-edge methods and protocols involving the molecular modeling of proteins

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras