Protein Structure Simulation Using Robotic Techniques

Document Type

Thesis Proposal

Advisors

Dr. Hans Dulimarta, dulimarh@gvsu.edu

Embargo Period

8-17-2010

Abstract

Molecular biology's biggest challenge today is in finding a way to accurately and quickly predict protein structure. Since a protein's structure determines its function, this knowledge is vital in understanding what a protein does. Currently, only an actual picture of a protein made using x-ray crystallography can show its structure but this method is expensive and can not be used for all proteins. Computer simulations have been tried and a structural approach, which attempts to determine the structure from its amino acid sequence alone, has shown some promise. An intriguing variation of this approach uses robotic motion planning techniques, specifically random path planning, in trying to create a faster and more accurate model. The key insight of this approach is in realizing that a protein can be viewed as a semi-rigid chain with two degrees of freedom at each link, similar to a robot arm with multiple degrees of freedom. Since robot arms must be moved in real time, there has been a great deal of research into calculating their possible configurations quickly and this has been ingeniously and productively applied to the problem of protein structure. As my research, I plan to explore and replicate this technique, trying to find its strengths and limitations by experimenting with different proteins of known structure. In addition, I hope to attempt to extend the technique, depending on the results of my experiments, possibly using parallel processing techniques or other robotic techniques to speed up the algorithm.

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