Molecular Modeling of Proteins

• 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.

From the reviews:"This book covers many different aspects of protein modeling and is just one volume in an extremely large series … . might be useful as an overview of the various techniques and methods used for the molecular modeling of proteins." (Andrzej Kloczkowski and Robert L. Jernigan, Journal of the American Chemical Society, Vol. 130 (37), 2008)