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Monte Carlo applications for creation of new ensembles and thermodynamic analysis of the biomolecular interaction

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João Victor de Souza Cunha
Total Authors: 1
Document type: Master's Dissertation
Press: São Carlos.
Institution: Universidade de São Paulo (USP). Instituto de Física de São Carlos (IFSC/BT)
Defense date:
Examining board members:
Alessandro Silva Nascimento; Andrei Leitão; Gustavo de Miranda Seabra
Advisor: Alessandro Silva Nascimento

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 drug design. The free energy of binding is the 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 evaluate a computationally inexpensive model which can improve the results from molecular docking simulations. For this end, the Monte Carlo method is implemented to sample different ligand configurations inside the macromolecular binding site. The evaluation of this methodology showed that is possible to calculate entropy and enthalpy, along analyzing the interactive capacity between receptor-ligands complexes in a satisfactory way for the bacteriophage T4. (AU)