Monte Carlo applications in a docking algorithim for creation of new ensembles and free energy calculation

Abstract

The molecular interactions, especially the ones with a non-covalent nature, are key processes in general aspects of Cellular and Molecular Biology, including cellular communication and velocity and specificity of enzymatic reactions. So, there is a strong need for studies and development of methods for the calculation of the affinity on interaction processes, since these have a wide range of applications like rational planning of drugs. The free energy of binding is most important measure among the affinity measurements. It can be calculated by quick computational means, but lacking on strong theoretical basis or by complex calculations, using molecular dynamics, where one can compute accurate results but at the price of an increased computer power. The aim of this project is to present a third model, where solid statistical thermodynamics basis, but computationally inexpensive. This model relied on Monte-Carlo sampling and can be used as further step after molecular docking simulations. After the implementation of this algorithm and testing agains experimental data, we hope to obtain a new efficient and powerful tool for calculations of the free energy between proteins and small molecules of biotechnology and medical interest. (AU)