| Autor: |
Rashid Mahmood A, Newton MA Hakim, Hoque Md Tamjidul, Shatabda Swakkhar, Pham Duc, Sattar Abdul |
| Jazyk: |
angličtina |
| Rok vydání: |
2013 |
| Předmět: |
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| Zdroj: |
BMC Bioinformatics, Vol 14, Iss Suppl 2, p S16 (2013) |
| Druh dokumentu: |
article |
| ISSN: |
1471-2105 |
| DOI: |
10.1186/1471-2105-14-S2-S16 |
| Popis: |
Abstract Background Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3-dimensional face-centred-cubic lattice for structure mapping. For HP energy model, developing a compact hydrophobic-core (H-core) is essential for the progress of the search. The H-core helps find a stable structure with the lowest possible free energy. Results In order to build H-cores, we present a new Spiral Search algorithm based on tabu-guided local search. Our algorithm uses a novel H-core directed guidance heuristic that squeezes the structure around a dynamic hydrophobic-core centre. We applied random walks to break premature H-cores and thus to avoid early convergence. We also used a novel relay-restart technique to handle stagnation. Conclusions We have tested our algorithms on a set of benchmark protein sequences. The experimental results show that our spiral search algorithm outperforms the state-of-the-art local search algorithms for simplified protein structure prediction. We also experimentally show the effectiveness of the relay-restart. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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