MD-jeep: an implementation of a branch and prune algorithm for distance geometry problems

Authors:
Antonio Mucherino;Leo Liberti;Carlile Lavor
Affiliations:
INRIA Lille Nord Europe, Villeneuve d'Ascq, France;LIX, École Polytechnique, Palaiseau, France;Dept. of Applied Mathematics, State University of Campinas, Campinas, SP, Brazil
Venue:
ICMS'10 Proceedings of the Third international congress conference on Mathematical software
Year:
2010

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Abstract

We present MD-jeep, an implementation of a Branch & Prune (BP) algorithm, which we employ for the solution of distance geometry problems related to molecular conformations. We consider the problem of finding the conformation of a molecule from the distances between some pairs of its atoms, which can be estimated by experimental techniques. We reformulate this problem as a combinatorial optimization problem, and describe a branch and prune solution strategy. We discuss its software implementation, and its complexity in terms of floating-point operations and memory requirements. MD-jeep has been developed in the C programming language. The sources of the presented software are available on the Internet under the GNU General Public License (v.2).