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Finding Optimal Discretization Orders for Molecular Distance Geometry by Answer Set Programming

  • Douglas Gonçalves
  • Jacques Nicolas
  • Antonio Mucherino
  • Carlile Lavor
Chapter
Part of the Studies in Computational Intelligence book series (SCI, volume 610)

Abstract

The Molecular Distance Geometry Problem (MDGP) is the problem of finding the possible conformations of a molecule by exploiting available information about distances between some atom pairs. When particular assumptions are satisfied, the MDGP can be discretized, so that the search domain of the problem becomes a tree. This tree can be explored by using an interval Branch & Prune (iBP) algorithm. In this context, the order given to the atoms of the molecules plays an important role. In fact, the discretization assumptions are strongly dependent on the atomic ordering, which can also impact the computational cost of the iBP algorithm. In this work, we propose a new partial discretization order for protein backbones. This new atomic order optimizes a set of objectives, that aim at improving the iBP performances. The optimization of the objectives is performed by Answer Set Programming (ASP), a declarative programming language that allows to express our problem by a set of logical constraints. The comparison with previously proposed orders for protein backbones shows that this new discretization order makes iBP perform more efficiently.

Keywords

Total Order Protein Backbone Interval Distance Discretization Order Reference Atom 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We are thankful to the Brittany Region (France) and to the Brazilian research agencies FAPESP, CNPq for financial support.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Douglas Gonçalves
    • 1
  • Jacques Nicolas
    • 2
  • Antonio Mucherino
    • 3
  • Carlile Lavor
    • 4
  1. 1.CCFMUniversidade Federal de Santa CatarinaFlorianopolisBrazil
  2. 2.INRIARennes Bretagne AtlantiqueRennesFrance
  3. 3.IRISAUniversity of Rennes 1RennesFrance
  4. 4.IMECC-UNICAMPCampinasBrazil

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