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Review

Recent work in the development and application of protein–peptide docking

    Joseph Audie

    * Author for correspondence

    CMDBioscience, LLC, 5 Science Park, New Haven, CT 06511, USA.

    Sacred Heart University, Department of Chemistry, 5151 Park Avenue, Fairfield, CT 06825, USA

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    Email the corresponding author at joseph.audie@cmdbioscience.com

    &
    Jon Swanson

    ChemModeling LLC, Suite 101, 500 Huber Park Ct, Weldon Spring, MO 63304, USA

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    Published Online:23 Aug 2012https://doi.org/10.4155/fmc.12.99

    Abstract

    Interest in the development of novel peptide-based drugs is growing. There is, thus, a pressing need for the development of effective methods to enable novel peptide-based drug discovery. A cogent case can be made for the development and application of computational or in silico methods to assist with peptide discovery. In particular, there is a need for the development of effective protein–peptide docking methods. Here, recent work in the area of protein–peptide docking method development is reviewed and several drug-discovery projects that benefited from protein–peptide docking are discussed. In the present review, special attention is given to the search and scoring problems, the use of peptide docking to enable hit identification, and the use of peptide docking to help rationalize experimental results, and generate and test structure-based hypotheses. Finally, some recommendations are made for improving the future development and application of protein–peptide docking.

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