Distance geometry methods are used to turn a set of interatomic distances given by Nuclear Magnetic Resonance (NMR) experiments into a consistent molecular conformation. In a set of papers (see the survey [8]) we proposed a Branch-and-Prune (BP) algorithm for computing the set X of all incongruent embeddings of a given protein backbone. Although BP has a worst-case exponential running time in general, we always noticed a linear-like behaviour in computational experiments. In this chapter we provide a theoretical explanation to our observations. We show that the BP is fixed-parameter tractable on protein-like graphs and empirically show that the parameter is constant on a set of proteins from the Protein Data Bank.
CITATION STYLE
Liberti, L., Lavor, C., & Mucherino, A. (2013). The discretizable molecular distance geometry problem seems easier on proteins. In Distance Geometry: Theory, Methods, and Applications (Vol. 9781461451280, pp. 47–60). Springer New York. https://doi.org/10.1007/978-1-4614-5128-0_3
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