Double variable neighbourhood search with smoothing for the molecular distance geometry problem

Authors:
Leo Liberti;Carlile Lavor;Nelson Maculan;Fabrizio Marinelli
Affiliations:
École Polytechnique, LIX, Palaiseau, France 91128;Department of Applied Mathematics (IMECC-UNICAMP), State University of Campinas, Campinas, Brazil 13081-970;COPPE --- Systems Engineering, Federal University of Rio de Janeiro, Rio de Janeiro-RJ, Brazil 21941-972;École Polytechnique, LIX, Palaiseau, France 91128
Venue:
Journal of Global Optimization
Year:
2009

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Abstract

We discuss the geometrical interpretation of a well-known smoothing operator applied to the Molecular Distance Geometry Problem (MDGP), and we then describe a heuristic approach based on Variable Neighbourhood Search on the smoothed and original problem. This algorithm often manages to find solutions having higher accuracy than other methods. This is important as small differences in the objective function value may point to completely different 3D molecular structures.