Abstract
In this paper, we use integer programming approach for solving a hard combinatorial optimization problem, namely protein threading. For this sequence-to-structure alignment problem we apply cost-splitting technique to derive a new Lagrangian dual formulation. The optimal solution of the dual is sought by an algorithm of polynomial complexity. For most of the instances the dual solution provides an optimal or near-optimal (with negligible duality gap) alignment. The speed-up with respect to the widely promoted approach for solving the same problem in [17] is from 100 to 250 on computationally interesting instances. Such a performance turns computing score distributions, the heaviest task when solving PTP, into a routine operation.
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References
Akutsu, T., Miyano, S.: On the approximation of protein threading. Theoretical Computer Science 210, 261–275 (1999)
Andonov, R., Balev, S., Yanev, N.: Protein Threading Problem: From Mathematical Models to Parallel Implementations. INFORMS Journal on Computing 16(4), 393–405 (2004)
Balev, S.: Solving the Protein Threading Problem by Lagrangian Relaxation. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 182–193. Springer, Heidelberg (2004)
Fischer, D.: http://www.cs.bgu.ac.il/~dfishcer/CAFASP3/ (December 2002)
Caprara, A., Carr, R., Israil, S., Lancia, G., Walenz, B.: 1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap. Journal of Computational Biology 11(1), 27–52 (2004)
Greenberg, H., Hart, W., Lancia, G.: Opportunities for combinatorial optimization in computational biology. INFORMS Journal on Computing 16(3) (2004)
Ilog cplex, http://www.ilog.com/products/cplex
Lathrop, R.: The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059–1068 (1994)
Marin, A., Pothier, J., Zimmermann, K., Gibrat, J.-F.: FROST: A Filter Based Recognition Method. Proteins 49(4), 493–509 (2002)
Lengauer, T.: Computational biology at the beginning of the post-genomic era. In: Wilhelm, R. (ed.) Informatics: 10 Years Back - 10 Years Ahead. LNCS, vol. 2000, pp. 341–355. Springer, Heidelberg (2001)
Lancia, G.: Integer Programming Models for Computational Biology Problems. J. Comput. Sci. & Technol. 19(1), 60–77 (2004)
Lathrop, R.H., Smith, T.F.: Global optimum protein threading with gapped alignment and empirical pair potentials. J. Mol. Biol. 255, 641–665 (1996)
Nemhauser, G.L., Wolsey, L.A.: Integer and Combinatorial Optimization. Wiley, Chichester (1988)
Poirriez, V., Marin, A., Andonov, R., Gibrat, J.-F.: FROST: Revisited and Distributed, HiCOMB 2005. In: Fourth IEEE International Workshop on High Performance Computational Biology, Denver, CO (April 4, 2005)
R.: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2004) http://www.R-project.org
Setubal, J.C., Meidanis, J.: Introduction to computational molecular biology, ch. 8, pp. 252–259. Brooks/Cole Publishing Company, 511 Forest Lodge Road, Pacific Grove, CA 93950 (1997)
Xu, J., Li, M., Lin, G., Kim, D., Xu, Y.: RAPTOR: optimal protein threading by linear programming. Journal of Bioinformatics and Computational Biology 1(1), 95–118 (2003)
Xu, Y., Xu, D.: Protein threading using PROSPECT: design and evaluation. Proteins: Structure, Function, and Genetics 40, 343–354 (2000)
Yanev, N., Andonov, R.: Solving the protein threading problem in parallel. In: HiCOMB 2003 – Second IEEE International Workshop on High Performance Computational Biology, Avril, Nice, France (2003)
Yanev, N., Andonov, R.: Parallel Divide and Conquer Approach for the Protein Threading Problem. Concurrency and Computation: Practice and Experience 16, 961–974 (2004)
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Veber, P., Yanev, N., Andonov, R., Poirriez, V. (2005). Optimal Protein Threading by Cost-Splitting. In: Casadio, R., Myers, G. (eds) Algorithms in Bioinformatics. WABI 2005. Lecture Notes in Computer Science(), vol 3692. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557067_30
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DOI: https://doi.org/10.1007/11557067_30
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29008-7
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