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MD-jeep: An Implementation of a Branch and Prune Algorithm for Distance Geometry Problems

  • Antonio Mucherino
  • Leo Liberti
  • Carlile Lavor
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6327)

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).

Keywords

Protein Data Bank Penalty Function Binary Tree Atomic Position Molecular Conformation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Antonio Mucherino
    • 1
  • Leo Liberti
    • 2
  • Carlile Lavor
    • 3
  1. 1.INRIA Lille Nord Europe, Villeneuve d’AscqFrance
  2. 2.LIXÉcole PolytechniquePalaiseauFrance
  3. 3.Dept. of Applied MathematicsState University of CampinasCampinas-SPBrazil

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