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)
© 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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