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    DINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approach

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    Author
    Antunes, Dinler A.; Moll, Mark; Devaurs, Didier; Jackson, Kyle; Lizée, Gregory; More... Kavraki, Lydia E. Less...
    Date
    2017
    Abstract
    Molecular docking is a standard computational approach to predict binding modes of protein–ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays for ligands with more than 10 flexible bonds. This prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecules of growing interest in cancer research. To overcome this limitation, our group has previously proposed a meta-docking strategy, called DINC, to predict binding modes of large ligands. By incrementally docking overlapping fragments of a ligand, DINC allowed predicting binding modes of peptide-based inhibitors of transcription factors involved in cancer. Here, we describe DINC 2.0, a revamped version of the DINC webserver with enhanced capabilities and a more user-friendly interface. DINC 2.0 allows docking ligands that were previously too challenging for DINC, such as peptides with more than 25 flexible bonds. The webserver is freely accessible at http://dinc.kavrakilab.org, together with additional documentation and video tutorials. Our team will provide continuous support for this tool and is working on extending its applicability to other challenging fields, such as personalized immunotherapy against cancer.
    Citation
    Antunes, Dinler A., Moll, Mark, Devaurs, Didier, et al.. "DINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approach." Cancer Research, 77, no. 21 (2017) AACR: e55-e57. https://doi.org/10.1158/0008-5472.CAN-17-0511.
    Published Version
    https://doi.org/10.1158/0008-5472.CAN-17-0511
    Keyword
    DINC webserver; incremental algorithm; molecular docking; protein-peptide complexes
    Type
    Journal article
    Publisher
    AACR
    Citable link to this page
    https://hdl.handle.net/1911/102292
    Rights
    This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by AACR.
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    Home | FAQ | Contact Us | Privacy Notice | Accessibility Statement
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map