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BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex

  • Jeongyeon Seo
  • Jae-Kwan Kim
  • Joonghyun Ryu
  • Carlile Lavor
  • Antonio Mucherino
  • Deok-Soo Kim
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8360)

Abstract

The molecular distance geometry problem (MDGP) is a fundamental problem in determining molecular structures from the NMR data. We present a heuristic algorithm, the BetaMDGP, which outperforms existing algorithms for solving the MDGP. The BetaMDGP algorithm is based on the beta-complex, which is a geometric construct extracted from the quasi-triangulation derived from the Voronoi diagram of atoms. Starting with an initial tetrahedron defined by the centers of four closely located atoms, the BetaMDGP determines a molecular structure by adding one shell of atoms around the currently determined substructure using the beta-complex. The proposed algorithm has been entirely implemented and tested with atomic arrangements stored in an NMR format created from PDB files. Experimental results are also provided to show the powerful capability of the proposed algorithm.

Keywords

Protein structure determination Molecular Distance Geometry Problem Voronoi Diagram Quasi-triangulation Beta-complex 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Jeongyeon Seo
    • 1
  • Jae-Kwan Kim
    • 2
  • Joonghyun Ryu
    • 2
  • Carlile Lavor
    • 3
  • Antonio Mucherino
    • 4
  • Deok-Soo Kim
    • 1
    • 2
  1. 1.Department of Industrial EngineeringHanyang UniversitySeoulSouth Korea
  2. 2.Voronoi Diagram Research CenterHanyang UniversitySeoulSouth Korea
  3. 3.Dept. of Applied Math. (IMECC-UNICAMP)University of CampinasCampinasBrazil
  4. 4.IRISA, University of Rennes IFrance

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