Geometric Build-up Solutions for Protein Determination via Distance Geometry

Proteins carry out an almost innumerable amount of biological processes that are absolutely necessary to life and as a result proteins and their structures are very often the objects of study in research. As such, this thesis will begin with a description of protein function and structure, followed by brief discussions of the two major experimental structure determination methods. Another problem that often arises in molecular modeling is referred to as the Molecular Distance Geometry Problem (MDGP). This problem seeks to find coordinates for the atoms of a protein or molecule when given only a set of pair-wise distances between atoms. To introduce the complexities of the MDGP we begin at its origins in distance geometry and progress to the specific sub-problems and some of the solutions that have been developed. This is all in preparation for a discussion of what is known as the Geometric Build-up (GBU) Solution. This solution has lead to the development of several algorithms and continues to be modified to account for more and different complexities. The culmination of this thesis, then, is a new algorithm, the Revised Updated Geometric Build-up, that is faster than previous GBU’s while maintaining the accuracy of the resulting structure.

Name thesis:degree_name

Master of Science in Applied Mathematics

Discipline thesis:degree_discipline

Department of Mathematics and Computer Science

Year

2009

Author dc:creator

• Davis, Robert Tucker

Contributors dc:contributor

• Dr. Di Wu (Director), Dr. Claus Ernst, Dr. Claire A. Rinehart

• Molecular Distance Geometry Problem (MDGP)
• Geometric Build-up (GBU) Solution
• mathematical modeling of protein structure
• Applied Mathematics
• Biochemistry
• Molecular Biology
• Structural Biology

Repository record dc:identifier

https://digitalcommons.wku.edu/theses/102

OAI identifier oai:identifier

oai:digitalcommons.wku.edu:theses-1104