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

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dc.citation.firstpagee55en_US
dc.citation.issueNumber21en_US
dc.citation.journalTitleCancer Researchen_US
dc.citation.lastpagee57en_US
dc.citation.volumeNumber77en_US
dc.contributor.authorAntunes, Dinler A.en_US
dc.contributor.authorMoll, Marken_US
dc.contributor.authorDevaurs, Didieren_US
dc.contributor.authorJackson, Kyleen_US
dc.contributor.authorLizée, Gregoryen_US
dc.contributor.authorKavraki, Lydia E.en_US
dc.date.accessioned2018-06-27T13:50:15Zen_US
dc.date.available2018-06-27T13:50:15Zen_US
dc.date.issued2017en_US
dc.description.abstractMolecular 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.en_US
dc.identifier.citationAntunes, Dinler A., Moll, Mark, Devaurs, Didier, et al.. "DINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approach." <i>Cancer Research,</i> 77, no. 21 (2017) AACR: e55-e57. https://doi.org/10.1158/0008-5472.CAN-17-0511.en_US
dc.identifier.doihttps://doi.org/10.1158/0008-5472.CAN-17-0511en_US
dc.identifier.urihttps://hdl.handle.net/1911/102292en_US
dc.language.isoengen_US
dc.publisherAACRen_US
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by AACR.en_US
dc.subject.keywordDINC webserveren_US
dc.subject.keywordincremental algorithmen_US
dc.subject.keywordmolecular dockingen_US
dc.subject.keywordprotein-peptide complexesen_US
dc.titleDINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approachen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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