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Distance Geometry in Structural Biology: New Perspectives

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.

Keywords

  • Nuclear Magnetic Resonance
  • Simulated Annealing
  • Torsion Angle
  • Protein Data Bank
  • Nuclear Magnetic Resonance Data

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Fig. 16.1
Fig. 16.2

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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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Correspondence to Thérèse E. Malliavin .

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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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