Supercomputers in Modeling of Biological Systems

Supercomputers in Modeling of Biological Systems

Randall Maples (Oklahoma State University, USA), Sindhura Ramasahayam (Oklahoma State University, USA) and Gerard G. Dumancas (Oklahoma Medical Research Foundation, USA)
Copyright: © 2015 |Pages: 22
DOI: 10.4018/978-1-4666-7461-5.ch008
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Abstract

Modeling of biological systems has become an important facet in today's scientific community because it has aided in the simulation of the minute biological entities comprising a living individual. With the advent in the advances of supercomputers, most challenges in understanding the complexities of biological networks and processes occurring in the human body can now be understood. Proteins, which are large biomolecules comprised of amino acids, play a critical role in the proper functioning of a living organism, and, thus, the prediction of its structure is essential in medicine for drug design or in biotechnology, such as in the designing of novel enzymes. This chapter focuses on how supercomputers facilitate in the prediction of protein structures in its different forms, modeling of protein-ligand binding site identification, as well as in the protein-surface interactions modeling.
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Computational Methods For Protein Structure Prediction

The knowledge of the native protein structure could provide insights into its functions. Protein structures comprise of polymers of amino acids joined together by peptide bonds. Protein structures are classified into primary, secondary, and tertiary structures. The linear sequence of the polypeptide chain refers to its primary structure. The secondary structure is the polypeptide chain which comprises of α-helix and β-sheets or β-strands. The α-helix and β-strands are connected through coil or loop. Tertiary structure is the 3-D structure of the protein molecules in which α-helix and β-strands are folded into a compact globule.

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