Abstract
The protein folding structure prediction is computationally challenging and has been shown to be NP-hard when the 3D off-lattice AB model is employed. In this paper, the local adjustment tabu search (LATS) algorithm has been used to search the ground state of 3D AB off-lattice model for protein folding structure. A kind of optimization about the neighborhood scale and the annealing mechanism has been presented, where a local adjustment strategy has also been used to enhance the searching ability for the global minimum within theAB off-lattice model. Experimental results demonstrate that the proposed algorithm has better performance in global optimization and can predict 3D protein structure more effectively.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181, 223–227 (1973)
Lopes, H.S.: Evolutionary Algorithms for the Protein Folding Problem: A Review and Current Trends. In: Smolinski, T.G., Milanova, M.G., Hassanien, A.-E. (eds.) Computational Intelligence in Biomedicine and Bioinformatics. SCI, vol. 151, pp. 297–315. Springer, Heidelberg (2008)
Dill, K.A.: Theory for the folding and stability of globular proteins. Biochemistry 24, 1501–1509 (1985)
Hart, W.E., Newman, A.: Protein structure prediction with lattice models. In: Aluru, S. (ed.) Handbook of Molecular Biology. Computer and Information Science Series, pp. 1–24. Chapman & Hall/CRC Press (2006)
Irbäck, A., Peterson, C., Potthast, F., Sommelius, O.: Local interactions and protein folding: A three-dimensional off-lattice approach. J. Chem. Phys. 107, 273–282 (1997)
Stillinger, F.H.: Collective aspects of protein folding illustrated by a toy model. Phys. Rev. E 52, 2872–2877 (1995)
Bachmann, M., Arkin, H., Janke, W.: Multicanonical study of coarse-grained off-lattice models for folding heteropolymers. Phys. Rev. E 71, 31906 (2005)
Kim, S.-Y., Lee, S.B., Lee, J.: Structure optimization by conformational space annealing in an off-lattice protein model. Phys. Rev. E 72, 011916 (2005)
Hsu, H.-P., Mehra, V., Grassberger, P.: Structure optimization in an off-lattice protein model. Phys. Rev. E 68, 037703 (2003)
Zhu, H.B., Pu, C.D., Lin, X.L.: Protein structure prediction with EPSO in toy model. In: 2009 Second International Conference on Intelligent Networks and Intelligent Systems (2009)
Lin, X.L., Zhu, H.B.: Structure Optimization by an Improved Tabu Search in the AB Off-Lattice Protein Model. In: The 1st International Conference on Intelligent Networks and Intelligent Systems, pp. 123–126 (2008)
Lin, X.L., Yu, Z.H.: Effective Protein Folding Structure Prediction with the Local Adjustment Tabu Search Algorithm. In: ICMAI (2012)
Zhang, X.L., Lin, X.L.: Effective 3D Protein Structure Prediction With Local Adjustment Genetic-Annealing Algorithm. Interdiscip. Sci. Comput. Life Sci. 2, 1–7 (2010)
Zhang, X.L., Lin, X.L., Wan, C.P., Li, T.T.: Genetic-annealing algorithm for 3D off-lattice protein folding model. The 2nd BioDM Workshop on Data Mining for Biomedical Applications, PAKDD Workshops, 186–193 (2007)
Turkensteen, M., Andersen, K.A.: A Tabu Search Approach to Clustering. In: Operations Research Proceedings (2008)
Tariq, R., Yi, W., Kuo-Bin, L.: Multiple Sequence Alignment Using Tabu Search. In: Proc. Second Asia-Pacific Bioinformatics Conference (2004)
Lecchini-Visintini, A., Lygeros, J., Maciejowski, J.: Simulated Annealing: Rigorous finite-time guarantees for optimization on continuous domains. In: Advances in Neural Information Processing Systems 20, Proceedings of NIPS (2007)
Gatti, C.J., Hughes, R.E.: Optimization of Muscle Wrapping Objects Using Simulated Annealing. Annals of Biomedical Engineering 37, 1342–1347 (2009)
Liang, F.: Annealing contour Monte Carlo algorithm for structure optimization in an off-lattice protein model. J. Chem. Phys. 120, 6756 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Lin, X., Zhou, F. (2013). 3D Protein Structure Prediction with Local Adjust Tabu Search Algorithm. In: Huang, DS., Gupta, P., Wang, L., Gromiha, M. (eds) Emerging Intelligent Computing Technology and Applications. ICIC 2013. Communications in Computer and Information Science, vol 375. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39678-6_18
Download citation
DOI: https://doi.org/10.1007/978-3-642-39678-6_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-39677-9
Online ISBN: 978-3-642-39678-6
eBook Packages: Computer ScienceComputer Science (R0)