Molecular Modeling of Proteins

Molecular modeling has undergone a remarkable transformation in the last 20 years. This book 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 the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.

Provides step-by-step protocols presented by world renowned experts in the field Contains authoritative reviews of methods applicable to protein modeling Enables readers to apply state-of-the-art methods to their own research Contains links to downloadable software made available by the authors Includes supplementary material: sn.pub/extras

Inhalt
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 ProteinLigand 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.