Parallel evolution strategy for protein threading.

Date of Award


Degree Type


Degree Name



Computer Science


Computer Science.




A protein-sequence folds into a specific shape in order to function in its aqueous state. If the primary sequence of a protein is given, what is its three dimensional structure? This is a long-standing problem in the field of molecular biology and it has large implication to drug design and cure. Among several proposed approaches, protein threading represents one of the most promising technique. The protein threading problem (PTP) is the problem of determining the three-dimensional structure of a given but arbitrary protein sequence from a set of known structures of other proteins. This problem is known to be NP-hard and current computational approaches to threading are time-consuming and data-intensive. In this thesis, we proposed an evolution strategy (ES) based approach for protein threading (EST). We also developed two parallel approaches for the PTP problem and both are parallelizations of our novel EST. The first method, we call SQST-PEST (Single Query Single Template Parallel EST) threads a single query against a single template. We use ES to find the best alignment between the query and the template, and ES is parallelized. The second method, we call SQMT-PEST (Single Query Multiple Templates Parallel EST) to allow for threading a single query against multiple templates within reasonable time. We obtained better results than current comparable approaches, as well as significant reduction in execution time.Dept. of Computer Science. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis2005 .I85. Source: Masters Abstracts International, Volume: 44-03, page: 1403. Thesis (M.Sc.)--University of Windsor (Canada), 2005.