Application of tabu search strategy for finding low energy structure of protein

Authors:
Jacek Błaewicz;Piotr Łukasiak;Maciej Miłostan
Affiliations:
Institute of Computing Science, Poznań University of Technology, Piotrowo 3a, 60-965 Poznań, Poland and Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12, 61- ...;Institute of Computing Science, Poznań University of Technology, Piotrowo 3a, 60-965 Poznań, Poland and Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12, 61- ...;Institute of Computing Science, Poznań University of Technology, Piotrowo 3a, 60-965 Poznań, Poland
Venue:
Artificial Intelligence in Medicine
Year:
2005

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Abstract

Objective:: Understanding protein functionality would mean understanding the basics of life. This functionality follows a three-dimensional structure of proteins. Unfortunately till now it is not possible to obtain these structures artificially. This article offers a survey on the use of meta-heuristic methods in context of simplified models of protein folding. Methods:: Tabu search (TS) strategy is one of the most successful meta-heuristics that has been applied for large number of optimization problems. In the paper, the application of TS for finding low energy conformations of proteins in a simplified lattice model has been proposed. Results:: The algorithm has been extensively tested and the tests showed its good performance. It compares well with the other heuristic approaches. Conclusions:: The approach presented is competitive as compared with other methods and due to its low computation time can be used as a complementary tool for an analysis of the three-dimensional protein structures.