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Simple folding model for HP lattice proteins

  • Molecular Modeling
  • Conference paper
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Bioinformatics (GCB 1996)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1278))

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Abstract

Combining the model of unguided, cotranslational folding of a nascent peptide chain with HP lattice proteins we designed a fast and straightforward folding algorithm. In choosing the search depth that is “looked ahead” at each chain growth step we tradeoff conformational search and accuracy against computational demands. We test the performance by folding short sequences with known, unique ground states. We find a success-rate, large enough to consider cotranslational foldability as a potential evolutionary fitness criterion. Characterizing the sequence to structure relation we find analogies to ground state ensembles: structure fitness landscapes are very rugged and there are few frequent and many rare structures. We conclude that our simple folding model is well suited for a realistic approximation of ensemble properties that we consider as crucial to understand the evolutionary dynamics of biopolymers.

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Author information

Authors and Affiliations

  1. Abteilung Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, ImNeuenheimerFeld 280, D-69120, Heidelberg

    Erich Bornberg-Bauer

  2. Institut für Mathematik der Universität Wien, A-1090, Wien

    Erich Bornberg-Bauer

Authors
  1. Erich Bornberg-Bauer
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Editor information

Ralf Hofestädt Thomas Lengauer Markus Löffler Dietmar Schomburg

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© 1997 Springer-Verlag Berlin Heidelberg

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Bornberg-Bauer, E. (1997). Simple folding model for HP lattice proteins. In: Hofestädt, R., Lengauer, T., Löffler, M., Schomburg, D. (eds) Bioinformatics. GCB 1996. Lecture Notes in Computer Science, vol 1278. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0033211

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  • DOI: https://doi.org/10.1007/BFb0033211

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-63370-9

  • Online ISBN: 978-3-540-69524-0

  • eBook Packages: Springer Book Archive

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