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Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores

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Principles and Practice of Constraint Programming — CP 2001 (CP 2001)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2239))

Abstract

Lattice protein models are used for hierarchical approaches to protein structure prediction, as well as for investigating principles of protein folding. So far, one has the problem that there exists no lattice that can model real protein conformations with good quality and for which an efficient method to find native conformations is known.

We present the first method for the FCC-HP-Model [3] that is capable of finding native conformations for real-sized HP-sequences. It has been shown [23] that the FCC lattice can model real protein conformations with coordinate root mean square deviation below 2 Å.

Our method uses a constraint-based approach. It works by first calculating maximally compact sets of points (hydrophobic cores), and then threading the given HP-sequence to the hydrophobic cores such that the core is occupied by H-monomers.

Supported by the PhD programme “Graduiertenkolleg Logik in der Informatik” (GKLI) of the “Deutsche Forschungsgemeinschaft” (DFG).

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Authors and Affiliations

  1. Institut für Informatik, LMU München, Oettingenstra\e 67, D-80538, München, Germany

    Rolf Backofen & Sebastian Will

Authors
  1. Rolf Backofen
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  2. Sebastian Will
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Editor information

Editors and Affiliations

  1. Department of Computer Science, The University of York, YO10 5DD, Heslington, York, UK

    Toby Walsh

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Backofen, R., Will, S. (2001). Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. In: Walsh, T. (eds) Principles and Practice of Constraint Programming — CP 2001. CP 2001. Lecture Notes in Computer Science, vol 2239. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45578-7_34

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  • DOI: https://doi.org/10.1007/3-540-45578-7_34

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42863-3

  • Online ISBN: 978-3-540-45578-3

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