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Distance Geometry in Structural Biology: New Perspectives

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Distance Geometry

Abstract

Proteins are polypeptides of amino acids involved in most of the biological processes. In the last 50 years, the study of their structures at the molecular level revolutioned the vision of biology. The three-dimensional structure of these molecules helps in the identification of their biological function. In this chapter, we focus our attention on methods for structure determination based on distance information obtained by nuclear magnetic resonance (NMR) experiments. We give a few details about this experimental technique and we discuss the quality and the reliability of the information it is able to provide. The problem of finding protein structures from NMR information is known in the literature as the molecular distance geometry problem (MDGP). We review some of the historical and most used methods for solving MDGPs with NMR data. Finally, we give a brief overview of a new promising approach to the MDGP, which is based on a discrete formulation of the problem, and we discuss the perspectives this method could open in structural biology.

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Acknowledgements

This work is partially supported by the ANR project ANR-10-BINF-03-01, “Bip:Bip”. TM and MN acknowledge support by the CNRS and the Institut Pasteur.

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Authors and Affiliations

  1. Institut Pasteur, Paris, France

    Thérèse E. Malliavin & Michael Nilges

  2. IRISA, University of Rennes 1, avenue de General Leclerc, Rennes, 35042, France

    Antonio Mucherino

Authors
  1. Thérèse E. Malliavin
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  2. Antonio Mucherino
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  3. Michael Nilges
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Corresponding author

Correspondence to Thérèse E. Malliavin .

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Editors and Affiliations

  1. IRISA, University of Rennes 1, avenue du General Leclerc, Rennes, 35042, France

    Antonio Mucherino

  2. , Dept of Applied Maths (IMECC-UNICAMP), State University of Campinas, Campinas, 13081, Brazil

    Carlile Lavor

  3. , LIX, Ecole Polytechnique, Palaiseau, 91128, France

    Leo Liberti

  4. Instituto Alberto Luiz Coimbra de, Pos-Graduacao e Pesquisa de, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil

    Nelson Maculan

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Malliavin, T.E., Mucherino, A., Nilges, M. (2013). Distance Geometry in Structural Biology: New Perspectives. In: Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds) Distance Geometry. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-5128-0_16

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