IDEAS home Printed from https://ideas.repec.org/h/spr/sprchp/978-1-4614-5128-0_3.html
   My bibliography  Save this book chapter

The Discretizable Molecular Distance Geometry Problem seems Easier on Proteins

In: Distance Geometry

Author

Listed:
  • Leo Liberti

    (LIX, École Polytechnique)

  • Carlile Lavor

    (University of Campinas, Department of Applied Maths)

  • Antonio Mucherino

    (University of Rennes 1, IRISA)

Abstract

Distance geometry methods are used to turn a set of interatomic distances given by Nuclear Magnetic Resonance (NMR) experiments into a consistent molecular conformation. In a set of papers (see the survey [8]) we proposed a Branch-and-Prune (BP) algorithm for computing the set X of all incongruent embeddings of a given protein backbone. Although BP has a worst-case exponential running time in general, we always noticed a linear-like behaviour in computational experiments. In this chapter we provide a theoretical explanation to our observations. We show that the BP is fixed-parameter tractable on protein-like graphs and empirically show that the parameter is constant on a set of proteins from the Protein Data Bank.

Suggested Citation

  • Leo Liberti & Carlile Lavor & Antonio Mucherino, 2013. "The Discretizable Molecular Distance Geometry Problem seems Easier on Proteins," Springer Books, in: Antonio Mucherino & Carlile Lavor & Leo Liberti & Nelson Maculan (ed.), Distance Geometry, edition 127, chapter 0, pages 47-60, Springer.
    • Handle: RePEc:spr:sprchp:978-1-4614-5128-0_3
    DOI: 10.1007/978-1-4614-5128-0_3
    as

    Download full text from publisher

    To our knowledge, this item is not available for download. To find whether it is available, there are three options:
    1. Check below whether another version of this item is available online.
    2. Check on the provider's web page whether it is in fact available.
    3. Perform a
    for a similarly titled item that would be available.

    More about this item

    Keywords

    ;
    ;
    ;
    ;
    ;

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:sprchp:978-1-4614-5128-0_3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.