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Highly Flexible Protein-Peptide Docking Using CABS-Dock

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cris.lastimport.scopus2024-02-12T20:09:52Z
dc.abstract.enProtein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure is used. This chapter presents a successful CABS-dock use for docking a potentially therapeutic peptide to a protein target. Moreover, simulation contact maps, a new CABS-dock feature, are described and applied to the docking test case. Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/
dc.affiliationUniwersytet Warszawski
dc.contributor.authorKmiecik, Sebastian
dc.contributor.authorKozak, Konrad Jakub
dc.contributor.authorKoliński, Andrzej
dc.contributor.authorKurciński, Mateusz
dc.contributor.authorCiemny, Maciej
dc.date.accessioned2024-01-28T20:40:43Z
dc.date.available2024-01-28T20:40:43Z
dc.date.issued2017
dc.description.financeNie dotyczy
dc.identifier.doi10.1007/978-1-4939-6798-8_6
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/153540
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.publisher.ministerialHumana Press
dc.relation.bookModeling of Peptide-Protein Interactions-Methods in Molecular Biology : Methods and Protocols
dc.relation.pages69-94
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.subject.enCABS
dc.subject.enComputational modeling
dc.subject.enMolecular docking
dc.subject.enPeptide binding
dc.subject.enPeptide design
dc.subject.enProtein-peptide interactions
dc.titleHighly Flexible Protein-Peptide Docking Using CABS-Dock
dc.typeMonographChapter
dspace.entity.typePublication