Table of Contents

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.