Methodology -- Molecular Dynamics Simulations -- Monte Carlo Simulations -- Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes -- Comparison of Protein Force Fields for Molecular Dynamics Simulations -- Normal Modes and Essential Dynamics -- Free Energy Calculations -- Calculation of Absolute Protein–Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method -- Free Energy Calculations Applied to Membrane Proteins -- Molecular Modeling of Membrane Proteins -- Molecular Dynamics Simulations of Membrane Proteins -- Membrane-Associated Proteins and Peptides -- Implicit Membrane Models for Membrane Protein Simulation -- Protein Structure Determination -- Comparative Modeling of Proteins -- Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints -- Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes -- Conformational Change -- Conformational Changes in Protein Function -- Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations -- Modeling of Protein Misfolding in Disease -- Applications to Drug Design -- Identifying Putative Drug Targets and Potential Drug Leads -- Receptor Flexibility for Large-Scale In Silico Ligand Screens -- Molecular Docking.

Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. Molecular Modeling of Proteins provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists – especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in this book, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, Molecular Modeling of Proteins is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics.