KUKU

KU ScholarWorks

  • myKU
  • Email
  • Enroll & Pay
  • KU Directory
    • Login
    View Item 
    •   KU ScholarWorks
    • Molecular Biosciences
    • Molecular Biosciences Scholarly Works
    • View Item
    •   KU ScholarWorks
    • Molecular Biosciences
    • Molecular Biosciences Scholarly Works
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Structural templates for comparative protein docking

    Thumbnail
    View/Open
    Kundrotas_2015.pdf (1.070Mb)
    Issue Date
    2015-09
    Author
    Anishchenko, Ivan
    Kundrotas, Petras J.
    Tuzikov, Alexander V.
    Vakser, Ilya A.
    Publisher
    Wiley
    Type
    Article
    Article Version
    Scholarly/refereed, author accepted manuscript
    Rights
    This is the peer reviewed version of the following article: Anishchenko, I., Kundrotas, P. J., Tuzikov, A. V. and Vakser, I. A. (2015), Structural templates for comparative protein docking. Proteins, 83: 1563–1570. doi:10.1002/prot.24736, which has been published in final form at http://doi.org/10.1002/prot.24736. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
    Metadata
    Show full item record
    Abstract
    Structural characterization of protein-protein interactions is important for understanding life processes. Because of the inherent limitations of experimental techniques, such characterization requires computational approaches. Along with the traditional protein-protein docking (free search for a match between two proteins), comparative (template-based) modeling of protein-protein complexes has been gaining popularity. Its development puts an emphasis on full and partial structural similarity between the target protein monomers and the protein-protein complexes previously determined by experimental techniques (templates). The template-based docking relies on the quality and diversity of the template set. We present a carefully curated, non-redundant library of templates containing 4,950 full structures of binary complexes and 5,936 protein-protein interfaces extracted from the full structures at 12Å distance cut-off. Redundancy in the libraries was removed by clustering the PDB structures based on structural similarity. The value of the clustering threshold was determined from the analysis of the clusters and the docking performance on a benchmark set. High structural quality of the interfaces in the template and validation sets was achieved by automated procedures and manual curation. The library is included in the Dockground resource for molecular recognition studies at http://dockground.bioinformatics.ku.edu.
    URI
    http://hdl.handle.net/1808/23997
    DOI
    https://doi.org/10.1002/prot.24736
    Collections
    • Molecular Biosciences Scholarly Works [606]
    Citation
    Anishchenko, I., Kundrotas, P. J., Tuzikov, A. V. and Vakser, I. A. (2015), Structural templates for comparative protein docking. Proteins, 83: 1563–1570. doi:10.1002/prot.24736

    Items in KU ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.


    We want to hear from you! Please share your stories about how Open Access to this item benefits YOU.


    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
     

     

    Browse

    All of KU ScholarWorksCommunities & CollectionsThis Collection

    My Account

    Login

    Statistics

    View Usage Statistics

    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
     

     

    The University of Kansas
      Contact KU ScholarWorks
    Lawrence, KS | Maps
     
    • Academics
    • Admission
    • Alumni
    • Athletics
    • Campuses
    • Giving
    • Jobs

    The University of Kansas prohibits discrimination on the basis of race, color, ethnicity, religion, sex, national origin, age, ancestry, disability, status as a veteran, sexual orientation, marital status, parental status, gender identity, gender expression and genetic information in the University’s programs and activities. The following person has been designated to handle inquiries regarding the non-discrimination policies: Director of the Office of Institutional Opportunity and Access, IOA@ku.edu, 1246 W. Campus Road, Room 153A, Lawrence, KS, 66045, (785)864-6414, 711 TTY.

     Contact KU
    Lawrence, KS | Maps