Influence of pruning devices on the solution of molecular distance geometry problems

Authors:
Antonio Mucherino;Carlile Lavor;Therese Malliavin;Leo Liberti;Michael Nilges;Nelson Maculan
Affiliations:
CERFACS, Toulouse, France;IMECC, UNICAMP, Campinas, SP, Brazil;Institut Pasteur, Paris, France;LIX, École Polytechnique, Palaiseau, France;Institut Pasteur, Paris, France;COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
Venue:
SEA'11 Proceedings of the 10th international conference on Experimental algorithms
Year:
2011

Citing 2
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Comparisons between an exact and a metaheuristic algorithm for the molecular distance geometry problem

Proceedings of the 11th Annual conference on Genetic and evolutionary computation
On the computation of protein backbones by using artificial backbones of hydrogens

Journal of Global Optimization

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Abstract

The Molecular Distance Geometry Problem (MDGP) is the problem of finding the conformation of a molecule from inter-atomic distances. In some recent work, we proposed the interval Branch & Prune (iBP) algorithm for solving instances of the MDGP related to protein backbones. This algorithm is based on an artificial ordering given to the atoms of the protein backbones which allows the discretization of the problem, and hence the applicability of the iBP algorithm. This algorithm explores a discrete search domain having the structure of a tree and prunes its infeasible branches by employing suitable pruning devices. In this work, we use information derived from Nuclear Magnetic Resonance (NMR) to conceive and add new pruning devices to the iBP algorithm, and we study their influence on the performances of the algorithm.