Biomolecular Simulations: Methods and Protocols

Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced.   Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.

Table of Contents:
Ab initio, Density Functional Theory, and Semi-empirical Calculations.-Ab initio Molecular Dynamics.-Introduction to QM/MM simulations.-Computational Enzymology.-QM and QM/MM Simulations of Proteins.-Classical Molecular Dynamics in a Nutshell.-Enhanced Sampling Algorithms.-Force Fields for Classical Molecular Dynamics.-Polarizable Force Fields.-Electrostatics Interactions in Classical Simulations.-An Introduction to Best Practices in Free EnergyCalculations.-Recipes for Free Energy Calculations in Biomolecular Systems.-Molecular Docking Methodologies.-Simulation Studies of the Mechanism of Membrane Transporters.-Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It.-Simulations of Lipid Monolayers.-Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation.-Simulation of Carbohydrates, From Molecular Docking to Dynamics in Water.-Systematic Methods for Structurally Consistent Coarse-grained Models.-The Martini Coarse-Grained Force Field.-Multiscale Molecular Modeling.-Coarse-grained Models for Protein Folding and Aggregation.-Elastic Network Models: Theoretical and Empirical Foundations.-An Introduction to Dissipative Particle Dynamics.-Multiscale Molecular Dynamics Simulations of Membrane Proteins.-Vesicles and Vesicle Fusion: Coarse-grained Simulations.