Estimation of distributed algorithms for ab initio prediction of protein structures

• Grant number: 10/02928-2
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: July 01, 2011
• End date: October 31, 2014
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computer Systems
• Principal Investigator: Alexandre Cláudio Botazzo Delbem
• Grantee: Daniel Rodrigo Ferraz Bonetti
• Host Institution: Instituto de Ciências Matemáticas e de Computação (ICMC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated scholarship(s): 13/00919-4 - Estimation of distribution algorithms for ab initio protein structure prediction, BE.EP.DR

Abstract

Proteins are present in living beings and perform essential functions for the life process. The function that each protein performs in organism depends on its three-dimensional structure. Knowing the structure of an essential protein that causes a disease it is possible to develop medicines that inhibit disease-causing protein. However, finding the three-dimensional of the protein is known as one of biggest problem in Molecular Cell Biology today. Experimental methods as, for example, the X-Ray Crystallography and Nuclear Magnetic Resonance have been fundamental in the discovery of new proteins structures. However, these methods are costly and time consuming. This has encouraged researchers to use computational methods to predict protein structures. In general, computational methods have problems of efficiency and quality when applied to non-small proteins. Moreover, most computational methods use a priori knowledge to predict new structures and may lead to biased predictions. Thus, this project proposes to develop an Estimation of Distribution Algorithm (EDA) to predict protein structures using ab initio modeling. The EDA should be prepared in such a way that is able to find relationships between variables of the problem. Thus, the EDA can find protein structures efficiently and bias-free. (AU)

Academic Publications

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

BONETTI, Daniel Rodrigo Ferraz. Estimation of distribution algorithms for ab initio protein structure prediction. 2015. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Ciências Matemáticas e de Computação (ICMC/SB) São Carlos.