Abstract
The Molecular Distance Geometry Problem (MDGP) is the problem of finding the conformation of a molecule from inter-atomic distances. In some recent work, we proposed the interval Branch & Prune (iBP) algorithm for solving instances of the MDGP related to protein backbones. This algorithm is based on an artificial ordering given to the atoms of the protein backbones which allows the discretization of the problem, and hence the applicability of the iBP algorithm. This algorithm explores a discrete search domain having the structure of a tree and prunes its infeasible branches by employing suitable pruning devices. In this work, we use information derived from Nuclear Magnetic Resonance (NMR) to conceive and add new pruning devices to the iBP algorithm, and we study their influence on the performances of the algorithm.
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References
Berg, J.M., Tymoczko, J.L., Stryer, L.: Biochemistry, 6th edn. W.H. Freeman publications, New York (2006)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acid Research 28, 235–242 (2000)
Lavor, C., Liberti, L., Maculan, N.: The discretizable molecular distance geometry problem. Technical Report q-bio/0608012, arXiv (2006)
Lavor, C., Liberti, L., Maculan, N.: Molecular distance geometry problem. In: Floudas, C., Pardalos, P. (eds.) Encyclopedia of Optimization, 2nd edn., pp. 2305–2311. Springer, New York (2009)
Lavor, C., Liberti, L., Mucherino, A.: On the solution of molecular distance geometry problems with interval data. In: IEEE Conference Proceedings, International Workshop on Computational Proteomics, International Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong, pp. 77–82 (2010)
Lavor, C., Liberti, L., Mucherino, A.: The iBP algorithm for the discretizable molecular distance geometry problem with interval data (submitted) (Available on Optimization Online)
Lavor, C., Mucherino, A., Liberti, L., Maculan, N.: On the computation of protein backbones by using artificial backbones of hydrogens. To appear in Journal of Global Optimization (2011); Available online from July 24, 2010
Lavor, C., Mucherino, A., Liberti, L., Maculan, N.: Discrete approaches for solving molecular distance geometry problems using NMR data. International Journal of Computational Biosciences 1(1), 88–94 (2010)
Liberti, L., Lavor, C., Maculan, N.: A branch-and-prune algorithm for the molecular distance geometry problem. International Transactions in Operational Research 15, 1–17 (2008)
Liberti, L., Lavor, C., Mucherino, A., Maculan, N.: Molecular distance geometry methods: from continuous to discrete. International Transactions in Operational Research 18(1), 33–51 (2010)
Mielke, S.P., Krishnan, V.V.: An evaluation of chemical shift index-based secondary structure determination in proteins: influence of random coil chemical shifts. Journal of Biomolecular NMR 30(2), 143–196 (2004)
Mucherino, A., Lavor, C.: The branch and prune algorithm for the molecular distance geometry problem with inexact distances. In: Proceedings of the International Conference on Computational Biology, vol. 58, pp. 349–353. World Academy of Science, Engineering and Technology (2009)
Mucherino, A., Lavor, C., Liberti, L.: The Discretizable Distance Geometry Problem (submitted)
Mucherino, A., Liberti, L., Lavor, C., Maculan, N.: Comparisons between an exact and a metaheuristic algorithm for the molecular distance geometry problem. In: Rothlauf, F. (ed.) Proceedings of the Genetic and Evolutionary Computation Conference, Montreal, pp. 333–340. ACM, New York (2009)
Nilges, M., Gronenborn, A.M., Brunger, A.T., Clore, G.M.: Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Engineering 2, 27–38 (1988)
Saxe, J.B.: Embeddability of weighted graphs in k-space is strongly NP-hard. In: Proceedings of 17th Allerton Conference in Communications, Control and Computing, pp. 480–489 (1979)
Shen, Y., Delaglio, F., Cornilescu, G., Bax, A.: TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. Journal of Biomolecular NMR 44(4), 213–236 (2009)
Wishart, D.S., Sykes, B.D., Richards, F.M.: The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31(6), 1647–1698 (1992)
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Mucherino, A., Lavor, C., Malliavin, T., Liberti, L., Nilges, M., Maculan, N. (2011). Influence of Pruning Devices on the Solution of Molecular Distance Geometry Problems. In: Pardalos, P.M., Rebennack, S. (eds) Experimental Algorithms. SEA 2011. Lecture Notes in Computer Science, vol 6630. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20662-7_18
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DOI: https://doi.org/10.1007/978-3-642-20662-7_18
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