Molecular Modeling of Proteins

Chapter 1 Molecular dynamics simulations.

Chapter 2 Transition Path Sampling with Quantum/Classical Mechanics for Reaction Rates

Chapter 3 Current status of protein force fields for molecular dynamics simulations.

Chapter 5 Molecular Dynamics Simulations of Membrane Proteins

Chapter 6 Membrane-Associated Proteins and Peptides

Chapter 7 Coarse-grained force fields for molecular simulations.

Chapter 8 Tackling sampling challenges in biomolecular simulations.

Chapter 9 Calculation of Binding Free Energies

Chapter 10 The use of experimental structures to model protein dynamics.

Chapter 11 Computing ensembles of transitions with molecular dynamics simulations.

Chapter 12 Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter

Chapter 13 Simulations and Experiments in Protein Folding

Chapter 14 Comparative Modeling of Proteins

Chapter 15 De Novo Membrane Protein Structure Prediction

Chapter 16 NMR-Based Modeling and Refinement of Protein 3D Structures

Chapter 17 Methods for Predicting Protein–Ligand Binding Sites

Chapter 18 Information-Driven Structural Modelling of Protein–Protein Interactions

Chapter 19 Identifying putative drug targets and potential drug leads: starting points for virtual screening and docking.

Chapter 20 Molecular Docking to Flexible Targets