Date of Award

4-26-2007

Degree Type

Thesis

Degree Name

Computer Information Systems (M.S.)

Department

School of Computing and Information Systems

First Advisor

Hansye Dulimarta

Abstract

This approach to protein simulation uses Protein Data Bank information to construct useful, simple, geometric constraints that can be applied to a protein simulation. We compiled experimental data for proteins with between 30-90 residues and analyzed the relationship between their sizes, defined as the radius of a sphere that encloses the 3D structure; the maximum distance between any two residues and the number of residues in the protein. A significant relationship was found and the analysis was used to predict the ranges that the size and maximum distance between residues would have for a protein with a given number of residues. These ranges were used to constrain folding from secondary structures for proteins IROP and IHDD and, using a random path planning approach, produced results that were not terribly accurate, but quite fast, suggesting that the constraint would be most useful as an inexpensive addition to an existing technique.

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