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Transmembrane Protein Docking with JabberDock

Rudden, Lucas S. P. and Degiacomi, Matteo T. (2021) 'Transmembrane Protein Docking with JabberDock.', Journal of chemical information and modeling., 61 (3). pp. 1493-1499.

Abstract

Transmembrane proteins act as an intermediary for a broad range of biological process. Making up 20% to 30% of the proteome, their ubiquitous nature has resulted in them comprising 50% of all targets in drug design. Despite their importance, they make up only 4% of all structures in the PDB database, primarily owing to difficulties associated with isolating and characterizing them. Membrane protein docking algorithms could help to fill this knowledge gap, yet only few exist. Moreover, these existing methods achieve success rates lower than the current best soluble proteins docking software. We present and test a pipeline using our software, JabberDock, to dock membrane proteins. JabberDock docks shapes representative of membrane protein structure and dynamics in their biphasic environment. We verify JabberDock’s ability to yield accurate predictions by applying it to a benchmark of 20 transmembrane dimers, returning a success rate of 75.0%. This makes our software very competitive among available membrane protein–protein docking tools.

Item Type:Article
Full text:(AM) Accepted Manuscript
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Status:Peer-reviewed
Publisher Web site:https://doi.org/10.1021/acs.jcim.0c01315
Publisher statement:This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Information and Modeling, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jcim.0c01315
Date accepted:No date available
Date deposited:07 April 2021
Date of first online publication:26 February 2021
Date first made open access:26 February 2022

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