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    Global and local structural similarity in protein–protein complexes: Implications for template-based docking

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    Kondrotas_2013.pdf (689.8Kb)
    Issue Date
    2013-12
    Author
    Kundrotas, Petras J.
    Vasker, Ilya A.
    Publisher
    Wiley
    Type
    Article
    Article Version
    Scholarly/refereed, author accepted manuscript
    Rights
    This is the peer reviewed version of the following article: Proteins, which has been published in final form at http://dx.doi.org/10.1002/prot.24392. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
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    Abstract
    The increasing amount of structural information on protein–protein interactions makes it possible to predict the structure of protein–protein complexes by comparison/alignment of the interacting proteins to the ones in cocrystallized complexes. In the predictions based on structure similarity, the template search is performed by structural alignment of the target interactors with the entire structures or with the interface only of the subunits in cocrystallized complexes. This study investigates the scope of the structural similarity that facilitates the detection of a broad range of templates significantly divergent from the targets. The analysis of the target-template similarity is based on models of protein–protein complexes in a large representative set of heterodimers. The similarity of the biological and crystal packing interfaces, dissimilar interface structural motifs in overall similar structures, interface similarity to the full structure, and local similarity away from the interface were analyzed. The structural similarity at the protein–protein interfaces only was observed in ~25% of target-template pairs with sequence identity <20% and primarily homodimeric templates. For ~50% of the target-template pairs, the similarity at the interface was accompanied by the similarity of the whole structure. However, the structural similarity at the interfaces was still stronger than that of the noninterface parts. The study provides insights into structural and functional diversity of protein–protein complexes, and relative performance of the interface and full structure alignment in docking.
    URI
    http://hdl.handle.net/1808/23519
    DOI
    https://doi.org/10.1002/prot.24392
    Collections
    • Molecular Biosciences Scholarly Works [581]
    Citation
    Kundrotas, P. J., & Vakser, I. A. (2013). Global and local structural similarity in protein–protein complexes: Implications for template-based docking. Proteins, 81(12), 2137–2142. http://doi.org/10.1002/prot.24392

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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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