Evolutionary algorithms and simplified models for tertiary protein structure prediction

Author(s)

Paulo Henrique Ribeiro Gabriel

• Document type: Master's Dissertation
• Press: São Carlos.
• Institution: Universidade de São Paulo (USP). Instituto de Ciências Matemáticas e de Computação (ICMC/SB)
• Defense date: 2010-03-23

Examining board members

Alexandre Cláudio Botazzo Delbem; Antonio Caliri; Rodrigo Fernandes de Mello

• Advisor: Alexandre Cláudio Botazzo Delbem

Abstract

Protein Structure Prediction (PSP) is a computationally complex problem. To overcome this drawback, simplified models of protein structures, such as the HP Model, together with Evolutionary Algorithms (EAs) have been investigated in order to find appropriate solutions for PSP. EAs with the HP Model have shown interesting results, however, they do not adequately evaluate potential solutions by using only the usual metric of hydrophobic contacts, hamming the performance of the algorithm. In this work, we present a multi-objective approach for PSP using HP Model that performs a better evaluation of the solutions by combining the evaluation based on the number of hydrophobic contacts with the distance among the hydrophobic amino acids. We employ a Multi-objective Evolutionary Algorithm based on Sub-population Tables (MEAT) to deal with these two metrics. MEAT can adequately explore the search space with relatively low number of individuals. As a consequence, the total assessments of the objective function is significantly reduced generating a method for PSP using HP Model that is faster and more robust (AU)

• FAPESP's process: 07/06928-4 - Developed of an Evolutionary Algorithm for Protein Tertiary Structure Prediction Problem
• Grantee: Paulo Henrique Ribeiro Gabriel
• Support Opportunities: Scholarships in Brazil - Master