An exploration of protein structure: Prediction, alignment, and theoretical interactions

The enigma surrounding protein structure is one of the most potentially useful open problems in the field of molecular biology. Proteins perform a vast array of functions within the cell, functions that are defined almost entirely by their structure, and yet their structure is extremely difficult to ascertain in silico. Many different computational approaches have been developed, most within the last decade, each with their own set of advantages and drawbacks. In this dissertation, contributions are made in three different areas surrounding protein structure. For the first area, protein structure prediction, an easily extensible homology modeling approach is demonstrated that is extremely efficient at comparing a protein sequence to a protein structural template. In the second area, protein structure-structure alignment, an enumerated algorithmic approach is shown that is able to perform alignment not only in an efficient manner, but in a way that is able to identify sub-domains regardless of their linear structure. Finally, in the third area, theoretical protein docking, a conceptual workflow is proposed and explored. This workflow allows biologists to quickly go from a protein primary sequence to that protein's potential docking sites that could bind inhibitors, substrates, or other interacting molecules.