On Suitable Orders For Discretizing Molecular Distance Geometry Problems Related To Protein Side Chains

Proteins are important molecules that are widely studied in biology. Their three-dimensional conformations can give clues about their function, however an optimal methodology for the identification of such conformations has not been found yet. Experiments of Nuclear Magnetic Resonance (NMR) are able to estimate distances between some pairs of atoms forming the protein, and the problem of identifying the possible conformations satisfying the available distance constraints is known in the scientific literature as the Molecular Distance Geometry Problem (MDGP). Since some years, some of us have been working on a suitable discretization for the MDGP and on an efficient Branch & Prune (BP) algorithm which is based on a tree search. In order to perform this discretization, however, some assumptions need to be satisfied. We recently hand-crafted a special order for protein backbone atoms which allows us to discretize all MDGPs concerning backbones. In this paper, we do the same for the side chains of some amino acids. Our computational experiments show that the inclusion of the side chain information allows to improve the performances of the BP algorithm. © 2012 Polish Info Processing Socit.379384Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., Bourne, P., The protein data bank (2000) Nucleic Acids Research, 28, pp. 235-242Crippen, G., Havel, T., (1988) Distance Geometry and Molecular Conforma-Tion, , John Wiley & Sons, New YorkLavor, C., Liberti, L., MacUlan, N., Mucherino, A., The discretizable molecular distance geometry problem (2012) Computational Optimization and Applications, 52, pp. 115-146Lavor, C., Liberti, L., MacUlan, N., Mucherino, A., Recent advances on the discretizable molecular distance geometry problem (2012) European Journal of Operational Research, 219, pp. 698-706Lavor, C., Liberti, L., Mucherino, A., The interval Branch-and-Prune Algorithm for the Discretizable Molecular Distance Geometry Problem with Inexact Distances (2011) To Appear in Journal of Global OptimizationLiberti, L., Lavor, C., MacUlan, N., A branch-and-prune algorithm for the molecular distance geometry problem (2008) International Transactions in Operational Research, 15, pp. 1-17Liberti, L., Lavor, C., Mucherino, A., MacUlan, N., Molecular distance geometry methods: From continuous to discrete (2010) International Transactions in Operational Research, 18, pp. 33-51Liberti, L., Masson, B., Lavor, C., Mucherino, A., Branch-and-prune trees with bounded width (2011) Proceedings of the 10th Cologne-Twente Workshop on Graphs and Combinatorial Optimization (CTW11), pp. 189-193. , Rome, ItalyNilges, M., Gronenborn, A., Brunger, A., Clore, G., Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. application to crambin (1988) Potato Carboxypeptidase Inhibitor and Barley Serine Proteinase Inhibitor 2, Protein Engineering, 2, pp. 27-38More, J., Wu, Z., Distance geometry optimization for protein structures (1999) Journal of Global Optimization, 15, pp. 219-234Mucherino, A., Lavor, C., Malliavin, T., Liberti, L., Nilges, M., MacUlan, N., Influence of pruning devices on the solution of molecular distance geometry problems (2011) Lecture Notes in Computer Science 6630, Proceedings of the 10th International Symposium on Experimental Algorithms (SEA11), pp. 206-217. , P.M. Pardalos and S. Rebennack (Eds.) Crete, GreeceSaxe, J., Embeddability of Weighted Graphs in k-Space is Strongly NP-hard (1979) Proceedings of 17th Allerton Conference in Communications, Control and Computing, pp. 480-48

On Suitable Orders for Discretizing Molecular Distance Geometry Problems related to Protein Side Chains

International audienceProteins are important molecules that are widely studied in biology. Their three-dimensional conformations can give clues about their function, however an optimal methodology for the identification of such conformations has not been found yet. Experiments of Nuclear Magnetic Resonance (NMR) are able to estimate distances between some pairs of atoms forming the protein, and the problem of identifying the possible conformations satisfying the available distance constraints is known in the scientific literature as the Molecular Distance Geometry Problem (MDGP). Since some years, some of us have been working on a suitable discretization for the MDGP and on an efficient Branch & Prune (BP) algorithm which is based on a tree search. In order to perform this discretization, however, some assumptions need to be satisfied. We recently hand-crafted a special order for protein backbone atoms which allows us to discretize all MDGPs concerning backbones. In this paper, we do the same for the side chains of some amino acids. Our computational experiments show that the inclusion of the side chain information allows to improve the performances of the BP algorithm