Monticelli L., Salonen E. (eds.) Biomolecular Simulations: Methods and Protocols

Humana Press, 2013. — 697 p. — ISBN: 1627030166.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.Quantum Mechanics Calculations
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 Mechanics: Atomistic Simulations
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 Energy Calculations
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
Simulations of Lipid Monolayers
Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation
Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water
Mesoscopic Simulations AND Coarse-Grained Models
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
An Introduction to Dissipative Particle Dynamics
Multiscale Molecular Dynamics Simulations of Membrane Proteins
Vesicles and Vesicle Fusion: Coarse-Grained Simulations