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. It continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, the usage of experimental data in combination with computational techniques, and 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.