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In this article we review the key modeling tools available for simulating biomolecular systems. We consider recent developments and representative applications of mixed quantum mechanics/molecular mechanics (QM/MM), elastic network models (ENMs), coarse-grained molecular dynamics, and grid-based tools for calculating interactions between essentially rigid protein assemblies. We consider how the different length scales can be coupled, both in a sequential fashion (e.g. a coarse-grained or grid model using parameterization from MD simulations), and via concurrent approaches, where the calculations are performed together and together control the progression of the simulation. We suggest how the concurrent coupling approach familiar in the context of QM/MM calculations can be generalized, and describe how this has been done in the CHARMM macromolecular simulation package.

Original publication

DOI

10.1016/j.sbi.2008.07.003

Type

Journal article

Journal

Curr Opin Struct Biol

Publication Date

10/2008

Volume

18

Pages

630 - 640

Keywords

Computational Biology, Computer Simulation, Elasticity, Electronics, Kinetics, Lipid Bilayers, Macromolecular Substances, Models, Molecular, Molecular Conformation, Proteins, Quantum Theory, Thermodynamics