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

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Transactions on Computational Science XXII

Part of the book series: Lecture Notes in Computer Science ((TCOMPUTATSCIE,volume 8360))

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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.

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Author information

Authors and Affiliations

  1. Department of Industrial Engineering, Hanyang University, 17 Haengdang-Dong, Sungdong-Ku, Seoul, 133-791, South Korea

    Jeongyeon Seo & Deok-Soo Kim

  2. Voronoi Diagram Research Center, Hanyang University, 17 Haengdang-Dong, Sungdong-Ku, Seoul, 133-791, South Korea

    Jae-Kwan Kim, Joonghyun Ryu & Deok-Soo Kim

  3. Dept. of Applied Math. (IMECC-UNICAMP), University of Campinas, 13081-970, Campinas, SP, Brazil

    Carlile Lavor

  4. IRISA, University of Rennes I, France

    Antonio Mucherino

Authors
  1. Jeongyeon Seo
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  2. Jae-Kwan Kim
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  3. Joonghyun Ryu
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  4. Carlile Lavor
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  5. Antonio Mucherino
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  6. Deok-Soo Kim
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Editors and Affiliations

  1. University of Calgary, AB, Canada

    Marina L. Gavrilova

  2. CloudFabriQ Ltd., London, UK

    C. J. Kenneth Tan

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Seo, J., Kim, JK., Ryu, J., Lavor, C., Mucherino, A., Kim, DS. (2014). BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex. In: Gavrilova, M.L., Tan, C.J.K. (eds) Transactions on Computational Science XXII. Lecture Notes in Computer Science, vol 8360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-54212-1_7

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  • DOI: https://doi.org/10.1007/978-3-642-54212-1_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-54211-4

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