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    Docking by structural similarity at protein-protein interfaces

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    Kondrotas_2011.pdf (1.828Mb)
    Issue Date
    2010-11-15
    Author
    Sinha, Rohita
    Kundrotas, Petras J.
    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: Proteins, which has been published in final form at http://dx.doi.org/10.1002/prot.22812. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
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    Abstract
    Rapid accumulation of experimental data on protein-protein complexes drives the paradigm shift in protein docking from ‘traditional,’ template free approaches to template based techniques. Homology docking algorithms based on sequence similarity between target and template complexes can account for up to 20% of known protein-protein interactions. When highly homologous templates for the target complex are not available, but the structure of the target monomers is known, docking by local structural alignment may provide an adequate solution. Such an algorithm was developed based on the structural comparison of monomers to co-crystallized interfaces. A library of the interfaces was generated from co-crystallized protein-protein complexes in PDB. The partial structure alignment algorithm was validated on the Dockground benchmark sets. The optimal performance of the partial (interface) structure alignment was achieved with the interface residues defined by 12Å distance across the interface. Overall, the partial structural alignment yielded more accurate models than the full structure alignment. Most templates identified by the partial structural alignment had low sequence identity to the target, which makes them hard to detect by sequence-based methods. The results indicate that the structure alignment techniques provide a much needed addition to the docking arsenal, with the combined structural alignment and template free docking success rate significantly surpassing that of the free docking alone.
    URI
    http://hdl.handle.net/1808/23518
    DOI
    https://doi.org/10.1002/prot.22812
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    • Molecular Biosciences Scholarly Works [581]
    Citation
    Sinha, R., Kundrotas, P. J., & Vakser, I. (2010). Docking by structural similarity at protein-protein interfaces. Proteins, 78(15), 3235–3241. http://doi.org/10.1002/prot.22812

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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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