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Home / Graduate / M.S. Theses Completed
  Rabun Koşar, 2003    

Thesis Title

Applying genetic algorithms to inverse protein folding problem


Finding the three dimensional structure of protein is currently the most important question in bioinformatics area. Together with it is the inverse folding problem; given the structure of the protein, find the sequences that are compliant with it. Given the fact that there are far less number of structures than sequences, this problem is more plausible to solve. We have implemented a genetic algorithm (GA) to solve this problem. The algorithm tries to minimize the free energy by trying to find highly probable residuals together in probability terms in order to form suitable structure.The efficiency of the algorithm is tested by different ways. First the results are compared to sequences in databases to find similar sequences. Then the sequence is threaded to target fold to find whether it is in fact compatible with the target or not. Since this is possible when the threading gives minimum energy state for the target and other folds are not in close states, a comparison is possible. We can find highly plausible sequences for a given structure.
Boğaziçi University Department of Computer Engineering
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