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**Chapter 8** 

© 2012 Yunta, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use,

distribution, and reproduction in any medium, provided the original work is properly cited.

© 2012 Yunta, licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**Using Molecular Modelling to Study Interactions** 

To better understand the basis of the activity of any molecule with biological activity, it is important to know how this molecule interacts with its site of action, more specifically its conformational properties in solution and orientation for the interaction. Molecular recognition in biological systems relies on specific attractive and/or repulsive interactions between two partner molecules. This study seeks to identify such interactions between ligands and their host molecules, typically proteins, given their three-dimensional (3D) structures. Therefore, it is important to know about interaction geometries and approximate affinity contributions of attractive interactions. At the same time, it is necessary to be aware of the fact that molecular interactions behave in a highly non-additive fashion. The same interaction may account for different amounts of free energy in different contexts and any change in molecular structure might have multiple effects, so it is only reliable to compare similar structures. In fact, the multiple interactions present in a single two-molecule complex are a compromise between attractive and repulsive interactions. On the other hand, a molecular complex is not characterised by a single structure, as can be seen in crystal structures, but by an ensemble of structures. Furthermore, changes in the degree of freedom of both partners during an

interaction have a large impact on binding free energy [Bissantz et al., 2010].

The availability of high-quality molecular graphics tools in the public domain is changing the way macromolecular structure is perceived by researchers, while computer modelling has emerged as a powerful tool for experimental and theoretical investigations. Visualisation of experimental data in a 3D, atomic-scale model can not only help to explain unexpected results but often raises new questions, thereby affecting future research. Models of sufficient quality can be set in motion in molecular dynamic (MD) simulations to move beyond a static picture and provide insight into the dynamics of important biological

**Between Molecules with Biological Activity** 

María J. R. Yunta

**1. Introduction** 

processes.

http://dx.doi.org/10.5772/54007

Additional information is available at the end of the chapter
