Hydrophobic-Hydrophilic Forces and their Effects on Protein Structural Similarity
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Hydrophobic-Hydrophilic interactions have a strong impact on the three-dimensional structure a protein will adopt. Because structure, not amino acid sequence order, carry out certain functions it is important to understand how these forces affect the protein folding process. In recent years, a lot of focus has been dedicated towards ab initio protein folding prediction, which tries to predict a proteins native conformation from its sequence alone. To aid this type of prediction sub-conformations from already known proteins are used to limit the free energy conformational search space. In this paper we looked into the subconformations' hydrophobic-hydrophilic nature by incorporating a HP model and proposed a way of evaluating how these type of forces affect the protein folding process. By doing this, we can gain insight into how hydrophobic-hydrophilic interactions affect protein structural similarity, and thus aid us in picking more suitable sub-conformations based off their HP shape for use in protein structure prediction.
Supplementary Proceedings [of the] Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008)
Copyright 2008 PRIB. The attached file is reproduced here in accordance with the copyright policy of the publisher. Please refer to the conference's website for access to the definitive, published version.
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