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Fragment-Based Computational Protein Structure Prediction

Authors:
Nashat Mansour
Meghrig Terzian

Keywords: protein structure prediction; scatter search; CHARMM36; protein fragments.

Abstract:
Proteins consist of sequences of amino acids that fold into 3-dimensional structures. The 3-dimensional configuration determines a protein’s function. Hence, it is very important to determine the correct structure in order to identify the wrong folding that indicates a disease situation. Computational protein structure prediction methods have been proposed in order to alleviate the enormous time taken by wet-lab methods. This paper presents a fragment-based protein tertiary structure prediction method which employs the CHARMM36 energy model. The method is based on a two-phase Scatter Search algorithm that minimizes the energy function. Backbone fragments are extracted from the Robetta server and side chains are, extracted from the Dunbrack Library. The results show that the algorithm produces tertiary structures with promising root mean square deviations.

Pages: 108 to 112

Copyright: Copyright (c) IARIA, 2014

Publication date: August 24, 2014

Published in: conference

ISSN: 2308-4499

ISBN: 978-1-61208-354-4

Location: Rome, Italy

Dates: from August 24, 2014 to August 28, 2014