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

• Grant number: 14/01751-2
• Support Opportunities: Scholarships in Brazil - Master
• Start date: June 01, 2014
• End date: June 30, 2016
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Alessandro Silva Nascimento
• Grantee: João Victor de Souza Cunha
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated scholarship(s): 15/01709-9 - Binding free energy calculations for computational measurements of enthalpy and entropy in protein-ligand interactions, BE.EP.MS

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)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DE SOUZA, JOAO VICTOR; NOGUEIRA, VICTOR H. R.; NASCIMENTO, ALESSANDRO S.. Ligand binding free energy evaluation by Monte Carlo Recursion. COMPUTATIONAL BIOLOGY AND CHEMISTRY, v. 103, p. 12-pg., 2023-02-20. (17/18173-0, 20/03983-9, 14/06565-2, 10/15376-8, 14/01751-2, 15/01709-9, 15/26722-8)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

CUNHA, João Victor de Souza. Monte Carlo applications for creation of new ensembles and thermodynamic analysis of the biomolecular interaction. 2016. Master's Dissertation - Universidade de São Paulo (USP). Instituto de Física de São Carlos (IFSC/BT) São Carlos.