Molecular Modeling of Proteins [Hardcover]

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.

Molecular Dynamics Simulations.- Transition Path Sampling with Quantum/Classical Mechanics for Reaction Rates.- Current Status of Protein Force Fields for Molecular Dynamics Simulations.- Lipid Membranes for Membrane Proteins.- Molecular Dynamics Simulations of Membrane Proteins.- Membrane-Associated Proteins and Peptides.- Coarse-Grained Force Fields for Molecular Simulations.- Tackling Sampling Challenges in Biomolecular Simulations.- Calculation of Binding Free Energies.- The Use of Experimental Structures to Model Protein Dynamics.- Computing Ensembles of Transitions with Molecular Dynamics Simulations.- Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model NeurotrlÃ3