I am currently involved in two research projects that deal with computational methods in the search for global minimum energy conformations in protein folding. The objective of the research is to properly define a simplified energy potential and find the conformations that have the minimum energy according to the potential such that the conformations with minimal energy are geometrically close to the known native structures. We have developed a thermodynamic model of protein folding that incorporates both hydrophobicity and polar interactions. The model uses a united atom representation, but with polar hydrogens explicitly represented. We found our current spatial representation was acceptable for working with small proteins. But for larger proteins with more complex topology, especially when packing of secondary structures is involved, our current representation will lead most of the search to steric conflicts, thus dead ends. As the focus of the first research project, I am now developing a representation that takes into the flexibility of the protein chain into account, dynamically adjust the phi/psi values of the chain yet maintain the uniform coverage of the conformational space in the search. Based on the preliminary results in the research on spatial representations, I am also currently developping algorithms for constructing hydrophobic cores of protein structures from given protein sequences. The second project is the continuing efforts to maintain and upgrade the program GEOCORE. After the publication of the paper on GEOCORE, I have added new functionalities and improved the user interface. These include the capability of searching for the geometrically best conformations in the vast conformational space defined by a given set of phi/psi choices.
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