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A Pseudo de Bruijn Graph Representation for Discretization Orders for Distance Geometry

  • Antonio Mucherino
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9043)

Abstract

Instances of the distance geometry can be represented by a simple weighted undirected graph G. Vertex orders on such graphs are discretization orders if they allow for the discretization of the K-dimensional search space of the distance geometry. A pseudo de Bruijn graph B associated to G is proposed in this paper, where vertices correspond to (K + 1)-cliques of G, and there is an arc from one vertex to another if, and only if, they admit an overlap, consisting of K vertices of G. This pseudo de Bruijn graph B can be exploited for constructing discretization orders for G for which the consecutivity assumption is satisfied. A new atomic order for protein backbones is presented, which is optimal in terms of length.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Antonio Mucherino
    • 1
  1. 1.IRISAUniversity of Rennes 1RennesFrance

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