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International Work-Conference on Bioinformatics and Biomedical Engineering

IWBBIO 2019: Bioinformatics and Biomedical Engineering pp 3–13Cite as

A Coarse-Grained Representation for Discretizable Distance Geometry with Interval Data

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11465))

Abstract

We propose a coarse-grained representation for the solutions of discretizable instances of the Distance Geometry Problem (DGP). In several real-life applications, the distance information is not provided with high precision, but an approximation is rather given. We focus our attention on protein instances where inter-atomic distances can be either obtained from the chemical structure of the molecule (which are exact), or through experiments of Nuclear Magnetic Resonance (which are generally represented by real-valued intervals). The coarse-grained representation allows us to extend a previously proposed algorithm for the Discretizable DGP (DDGP), the branch-and-prune (BP) algorithm. In the standard BP, atomic positions are fixed to unique positions at every node of the search tree: we rather represent atomic positions by a pair consisting of a feasible region, together with a most-likely position for the atom in this region. While the feasible region is a constant during the search, the associated position can be refined by considering the new distance constraints that appear at further layers of the search tree. To perform the refinement task, we integrate the BP algorithm with a spectral projected gradient algorithm. Some preliminary computational experiments on artificially generated instances show that this new approach is quite promising to tackle real-life DGPs.

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Acknowledgments

AM and JHL wish to thank the CNRS and MoST for financial support (PRC project “Rapid NMR Protein Structure Determination and Conformational Transition Sampling by a Novel Geometrical Approach”). AM and DSG wish to thank CAPES PRINT for financial support. DSG also thanks CNPq for financial support (Grant n. 421386/2016-9).

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Authors and Affiliations

  1. IRISA, University of Rennes 1, Rennes, France

    Antonio Mucherino

  2. Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan

    Jung-Hsin Lin

  3. DM-CFM, Federal University of Santa Catarina, Florianópolis, Brazil

    Douglas S. Gonçalves

Authors
  1. Antonio Mucherino
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  2. Jung-Hsin Lin
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  3. Douglas S. Gonçalves
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Corresponding author

Correspondence to Jung-Hsin Lin .

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Editors and Affiliations

  1. Department of Computer Architecture and Computer Technology Higher Technical School of Information Technology and Telecommunications Engineering, CITIC-UGR, Granada, Spain

    Ignacio Rojas

  2. ETSIIT, University of Granada, Granada, Spain

    Olga Valenzuela

  3. CITIC-UGR, University of Granada, Granada, Spain

    Fernando Rojas

  4. Fundacion Progreso y Salud, Granada, Spain

    Francisco Ortuño

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Mucherino, A., Lin, JH., Gonçalves, D.S. (2019). A Coarse-Grained Representation for Discretizable Distance Geometry with Interval Data. In: Rojas, I., Valenzuela, O., Rojas, F., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2019. Lecture Notes in Computer Science(), vol 11465. Springer, Cham. https://doi.org/10.1007/978-3-030-17938-0_1

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  • DOI: https://doi.org/10.1007/978-3-030-17938-0_1

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-17937-3

  • Online ISBN: 978-3-030-17938-0

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