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Journal of Global Optimization

, Volume 50, Issue 2, pp 329–344 | Cite as

On the computation of protein backbones by using artificial backbones of hydrogens

  • C. Lavor
  • A. Mucherino
  • L. Liberti
  • N. Maculan
Article

Abstract

NMR experiments provide information from which some of the distances between pairs of hydrogen atoms of a protein molecule can be estimated. Such distances can be exploited in order to identify the three-dimensional conformation of the molecule: this problem is known in the literature as the Molecular Distance Geometry Problem (MDGP). In this paper, we show how an artificial backbone of hydrogens can be defined which allows the reformulation of the MDGP as a combinatorial problem. This is done with the aim of solving the problem by the Branch and Prune (BP) algorithm, which is able to solve it efficiently. Moreover, we show how the real backbone of a protein conformation can be computed by using the coordinates of the hydrogens found by the BP algorithm. Formal proofs of the presented results are provided, as well as computational experiences on a set of instances whose size ranges from 60 to 6000 atoms.

Keywords

Distance geometry Protein molecules Hydrogen atoms Combinatorial optimization Branch and Prune 

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Copyright information

© Springer Science+Business Media, LLC. 2010

Authors and Affiliations

  • C. Lavor
    • 1
  • A. Mucherino
    • 2
  • L. Liberti
    • 3
  • N. Maculan
    • 4
  1. 1.Department of Applied Mathematics (IMECC-UNICAMP)State University of CampinasCampinasBrazil
  2. 2.INRIA Lille Nord EuropeVilleneuve d’AscqFrance
  3. 3.LIX, École PolytechniquePalaiseauFrance
  4. 4.COPPE, Systems EngineeringFederal University of Rio de JaneiroRio de JaneiroBrazil

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