Bringing folding pathways into strand pairing prediction

Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    7 Citations (Scopus)

    Abstract

    The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. In this work we report a new strand pairing algorithm. Our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming other strand pairs. We demonstrate that this approach provides an improvement over previously proposed algorithms.

    Original languageEnglish (US)
    Title of host publicationAlgorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
    Pages38-48
    Number of pages11
    StatePublished - Dec 24 2007
    Event7th International Workshop on Algorithms in Bioinformatics, WABI 2007 - PhiIadelphia, PA, United States
    Duration: Sep 8 2007 → Sep 9 2007

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume4645 LNBI
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Other

    Other7th International Workshop on Algorithms in Bioinformatics, WABI 2007
    CountryUnited States
    CityPhiIadelphia, PA
    Period9/8/07 → 9/9/07

    Fingerprint

    Folding
    Pairing
    Hydrogen
    Pathway
    Prediction
    Topology
    Hydrogen Bonds
    Hydrogen bonds
    Demonstrate

    All Science Journal Classification (ASJC) codes

    • Theoretical Computer Science
    • Computer Science(all)

    Cite this

    Jeong, J. K., Berman, P., & Przytycka, T. M. (2007). Bringing folding pathways into strand pairing prediction. In Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings (pp. 38-48). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4645 LNBI).
    Jeong, Jieun K. ; Berman, Piotr ; Przytycka, Teresa M. / Bringing folding pathways into strand pairing prediction. Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. 2007. pp. 38-48 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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    abstract = "The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. In this work we report a new strand pairing algorithm. Our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming other strand pairs. We demonstrate that this approach provides an improvement over previously proposed algorithms.",
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    year = "2007",
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    Jeong, JK, Berman, P & Przytycka, TM 2007, Bringing folding pathways into strand pairing prediction. in Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4645 LNBI, pp. 38-48, 7th International Workshop on Algorithms in Bioinformatics, WABI 2007, PhiIadelphia, PA, United States, 9/8/07.

    Bringing folding pathways into strand pairing prediction. / Jeong, Jieun K.; Berman, Piotr; Przytycka, Teresa M.

    Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. 2007. p. 38-48 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4645 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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    N2 - The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. In this work we report a new strand pairing algorithm. Our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming other strand pairs. We demonstrate that this approach provides an improvement over previously proposed algorithms.

    AB - The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. In this work we report a new strand pairing algorithm. Our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming other strand pairs. We demonstrate that this approach provides an improvement over previously proposed algorithms.

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    Jeong JK, Berman P, Przytycka TM. Bringing folding pathways into strand pairing prediction. In Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. 2007. p. 38-48. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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