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Updated: May 20, 2026

Spatial Separation of Molecular Conformers and Clusters
Published on: January 9, 2014
Exploiting symmetry properties of the discretizable molecular distance geometry problem
Antonio Mucherino1, Carlile Lavor, Leo Liberti
1IRISA, University of Rennes 1, Rennes, France. antonio.mucherino@irisa.fr
Abstract:
The Discretizable Molecular Distance Geometry Problem (DMDGP) involves a subset of instances of the distance geometry problem for which some assumptions allowing for discretization are satisfied. The search domain for the DMDGP is a binary tree that can be efficiently explored by employing a Branch & Prune (BP) algorithm. We showed in recent works that this binary tree may contain several symmetries, which are directly related to the total number of solutions of DMDGP instances. In this paper, we study the possibility of exploiting these symmetries for speeding up the solution of DMDGPs, and propose an extension of the BP algorithm that we named symmetry-driven BP (symBP). Computational experiments on artificial and protein instances are presented.
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