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Journal Articles Computational Optimization and Applications Year : 2012

The Discretizable Molecular Distance Geometry Problem

Abstract

Given a simple weighted undirected graph G=(V,E,d), the Molecular Distance Geometry Problem (MDGP) consists in finding an embedding x such that ||x_u - x_v|| = d(u,v) for each (u,v) in E. We show that under a few assumptions usually satisfied in proteins, the MDGP can be formulated as a search in a discrete space. We call this MDGP subclass the Discretizable MDGP (DMDGP). We show that the DMDGP is NP-hard and we propose a solution algorithm called Branch-and-Prune (BP). The BP algorithm performs remarkably well in practice in terms of speed and solution accuracy, and can be easily modified to find all incongruent solutions to a given DMDGP instance. We show computational results on several artificial and real-life instances.

Dates and versions

hal-00756940 , version 1 (24-11-2012)

Identifiers

Cite

Antonio Mucherino, Carlile Lavor, Leo Liberti, Nelson Maculan. The Discretizable Molecular Distance Geometry Problem. Computational Optimization and Applications, 2012, 24th International Federation for Information Processing-7th Technical Committee Conference on System Modeling and Optimization Jul 2009 Buenos Aires, 52, pp.115-146. ⟨10.1007/s10589-011-9402-6⟩. ⟨hal-00756940⟩
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