Predicting protein structure classes from function predictions

I. Sommer, J. Rahnenfuhrer, Ulrik de Lichtenberg, T. Lengauer

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting protein structure. The data on which our method is based comprise probabilities of functional categories; for given query sequences these probabilities are obtained by a neural net that has previously been trained on a variety of functionally important features. On a training set of sequences we assess the relevance of individual functional categories for identifying a given structural family. Using a combination of the most relevant categories, the likelihood of a query sequence to belong to a specific family can be estimated. Results: The performance of the method is evaluated using cross-validation. For a fixed structural family and for every sequence, a score is calculated that measures the evidence for family membership. Even for structural families of small size, family members receive significantly higher scores. For some examples, we show that the relevant functional features identified by this method are biologically meaningful. The proposed approach can be used to improve existing sequence-to-structure prediction methods.
    Original languageEnglish
    JournalBioinformatics
    Volume20
    Issue number5
    Pages (from-to)770
    ISSN1367-4803
    DOIs
    Publication statusPublished - 2004

    Cite this

    Sommer, I., Rahnenfuhrer, J., de Lichtenberg, U., & Lengauer, T. (2004). Predicting protein structure classes from function predictions. Bioinformatics, 20(5), 770. https://doi.org/10.1093/bioinformatics/btg483