Molecular modeling of proteins

Chapter 1 Molecular Dynamics Simulations

Chapter 2 Monte Carlo Simulations

Chapter 3 Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes

Chapter 4 Comparison of Protein Force Fields for Molecular Dynamics Simulations

Chapter 5 Normal Modes and Essential Dynamics

Chapter 6 Calculation of Absolute Protein–Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method

Chapter 7 Free Energy Calculations Applied to Membrane Proteins

Chapter 9 Membrane-Associated Proteins and Peptides

Chapter 10 Implicit Membrane Models for Membrane Protein Simulation

Chapter 11 Comparative Modeling of Proteins

Chapter 12 Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints

Chapter 13 Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

Chapter 14 Conformational Changes in Protein Function

Chapter 15 Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations

Chapter 16 Modeling of Protein Misfolding in Disease

Chapter 17 Identifying Putative Drug Targets and Potential Drug Leads

Chapter 18 Receptor Flexibility for Large-Scale In Silico Ligand Screens

Chapter 19 Molecular Docking