Researcher:
Güney, Emre

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Emre

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Güney

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Güney, Emre

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    Architectures and functional coverage of protein-protein interfaces
    (Elsevier, 2008) Nussinov, Ruth; Department of Chemical and Biological Engineering; Department of Computer Engineering; N/A; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Gürsoy, Attila; Güney, Emre; Keskin, Özlem; Faculty Member; Faculty Member; Master Student; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 245513; 8745; N/A; 26605
    The diverse range of cellular functions is performed by a limited number of protein folds existing in nature. One may similarly expect that cellular functional diversity would be covered by a limited number of protein-protein interface architectures. Here, we present 8205 interface clusters, each representing a unique interface architecture. This data set of protein-protein interfaces is analyzed and compared with older data sets. We observe that the number of both biological and crystal interfaces increases significantly compared to the number of Protein Data Bank entries. Furthermore, we find that the number of distinct interface architectures grows at a much faster rate than the number of folds and is yet to level off. We further analyze the growth trend of the functional coverage by constructing functional interaction networks from interfaces. The functional coverage is also found to steadily increase. Interestingly, we also observe that despite the diversity of interface architectures, some are more favorable and frequently used, and of particular interest, are the ones that are also preferred in single chains.
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    PublicationOpen Access
    HotSprint: database of computational hot spots in protein interfaces
    (Oxford University Press (OUP), 2008) Tunçbağ, Nurcan; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Güney, Emre; Keskin, Özlem; Gürsoy, Attila; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 26605; 8745
    We present a new database of computational hot spots in protein interfaces: HotSprint. Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. HotSprint contains data for 35 776 protein interfaces among 49 512 protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB) as of February 2006. The conserved residues in interfaces with certain buried accessible solvent area (ASA) and complex ASA thresholds are flagged as computational hot spots. The predicted hot spots are observed to correlate with the experimental hot spots with an accuracy of 76. Several machine-learning methods (SVM, Decision Trees and Decision Lists) are also applied to predict hot spots, results reveal that our empirical approach performs better than the others. A web interface for the HotSprint database allows users to browse and query the hot spots in protein interfaces; and it provides information for interface residues that are functionally and structurally important as well as the evolutionary history and solvent accessibility of residues in interfaces.