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Journal of Global Optimization

, Volume 71, Issue 4, pp 717–733 | Cite as

A symmetry-based splitting strategy for discretizable distance geometry problems

  • Felipe Fidalgo
  • Douglas S. Gonçalves
  • Carlile Lavor
  • Leo Liberti
  • Antonio Mucherino
Article
  • 104 Downloads

Abstract

Discretizable distance geometry problems consist in a subclass of distance geometry problems where the search space can be discretized and reduced to a tree. Such problems can be tackled by applying a branch-and-prune algorithm, which is able to perform an exhaustive enumeration of the solution set. In this work, we exploit the concept of symmetry in the search tree for isolating subtrees that are explored only one time for improving the algorithm performances. The proposed strategy is based on the idea of dividing an original instance of the problem into sub-instances that can thereafter be solved (almost) independently. We present some computational experiments on a set of artificially generated instances, with exact distances, to validate the theoretical results.

Keywords

Protein structure determination Partial reflection Decomposition Branch-and-prune 

Notes

Acknowledgements

FF, DG, CL and AM wish to thank FAPESP and CNPq for financial support. LL was partly supported by the ANR “Bip:Bip” project under contract ANR-10-BINF-0003.

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Authors and Affiliations

  1. 1.Department of MathematicsFederal University of Santa CatarinaBlumenauBrazil
  2. 2.Department of Mathematics, CFMFederal University of Santa CatarinaFlorianópolisBrazil
  3. 3.Department of Applied Mathematics (IMECC-UNICAMP)University of CampinasCampinasBrazil
  4. 4.CNRS LIXÉcole PolytechniquePalaiseauFrance
  5. 5.IRISAUniversité de Rennes 1RennesFrance

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