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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.
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https://hal.inria.fr/hal-00756940
Contributor : Antonio Mucherino <>
Submitted on : Saturday, November 24, 2012 - 1:24:59 PM
Last modification on : Tuesday, October 20, 2020 - 3:11:49 AM

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  • HAL Id : hal-00756940, version 1

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Antonio Mucherino, Carlile Lavor, Leo Liberti, Nelson Maculan. The Discretizable Molecular Distance Geometry Problem. Computational Optimization and Applications, Springer Verlag, 2012, 52, pp.115-146. ⟨hal-00756940⟩

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