Hydrophobic-Hydrophilic interactions have a strong impact on the three-dimensiol 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 tive conformation from its sequence alone. To aid this type of prediction sub-conformations from already known proteins are used to limit the free energy conformatiol search space. In this paper we looked into the subconformations' hydrophobic-hydrophilic ture 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.

Presented at Conferences

  • Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008) (2008)

    Melbourne , Australia