Molecular-dynamics Simulations of Biological Systems

Abstract

One of the main tools for studying biological molecules is the method of computer modelling based on molecular dynamics (MD). MD simulations provide detailed information about the fluctuations and conformational changes of proteins and nucleic acids. This method is routinely used for investigations of the structure, dynamics and thermodynamics of biological molecules and their complexes. In the literature, results of MD simulation of proteins dissolved in water, protein--DNA complexes and lipid systems, dealing with various aspects of the thermodynamics of ligand binding and folding and packaging of relatively small (short) proteins are continually published. Nowadays, there are many specialized techniques for solving particular problems, including those listed above, which take into account quantum-mechanical effects as well. The MD modelling technique is also widely used for determining the spatial structure of biological molecules by analyzing the information obtained by means of X-ray diffraction and nuclear magnetic resonance. ...