DNA and protein sequence data sets have exploded in size over the past several years and have stimulated the development of new methods for closing the sequence/structure gap. Bench laboratory methods, while being the most accurate, are still far too time consuming and limited to breech this gap. Thus computational methods have become the standard. The work described here details the development of a system to automatically select a structural template, align the template and query sequence and model the query. The system was implemented fully for antibodies but maintains a modular design that can accommodate a wider variety of molecule types. Extensive testing was performed using antibodies and the results of this analysis reveal the potential limitations of homology modeling and point toward ways to improve on the template selection method.

Library of Congress Subject Headings

Biochemical templates--Data processing; Amino acid sequence--Data processing; Homology theory

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Jiye Shi

Advisor/Committee Member

Gary Skuse


I, David R. Riley, hereby deny permission to the RIT Library of the Rochester Institute of Technology to reproduce my print thesis or dissertation in whole or in part until after 31 May 2007. Thereafter permission is granted.

Physical copy available from RIT's Wallace Library at QP517.B48 R45 2006


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