Protein Folding Prediction in a Cubic Lattice in Hydrophobic-Polar Model

The tertiary structure of the proteins determines their functions. Therefore, the predicting of protein's tertiary structure, based on the primary amino acid sequence from long time, is the most important and challenging subject in biochemistry, molecular biology, and biophysics. One of the mos...

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Bibliographic Details
Published in:Journal of computational biology Vol. 24; no. 5; p. 412
Main Authors: Yanev, Nicola, Traykov, Metodi, Milanov, Peter, Yurukov, Borislav
Format: Journal Article
Language:English
Published: United States 01.05.2017
Subjects:
Algorithms
Amino Acid Sequence
Amino Acids - chemistry
Computational Biology - methods
Hydrophobic and Hydrophilic Interactions
Models, Molecular
Monte Carlo Method
Protein Conformation
Protein Folding
Protein Structure, Tertiary
Proteins - chemistry
protein folding
3D lattice
heuristics
HP model
bioinformatics
mixed integer programming
ISSN:1557-8666, 1557-8666
Online Access:Get more information
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Summary:The tertiary structure of the proteins determines their functions. Therefore, the predicting of protein's tertiary structure, based on the primary amino acid sequence from long time, is the most important and challenging subject in biochemistry, molecular biology, and biophysics. One of the most popular protein structure prediction methods, called Hydrophobic-Polar (HP) model, is based on the observation that in polar environment hydrophobic amino acids are in the core of the molecule-in contact between them and more polar amino acids are in contact with the polar environment. In this study, we present a new mixed integer programming formulation, exact algorithm, and two heuristic algorithms to solve the protein folding problem stated as a combinatorial optimization problem in a simple cubic lattice. The results from computational runs on a set of benchmarks are favorably compared to known algorithms for solving the 3D lattice HP model as genetic algorithms, ant colony optimization algorithm, and Monte Carlo algorithm.
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ISSN:1557-8666
1557-8666
DOI:10.1089/cmb.2016.0181