Molecular Modeling of Proteins

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... Mehr