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Transmembrane Protein Docking with JabberDock

Rudden, Lucas S.P.; Degiacomi, Matteo T.

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Authors

Lucas S.P. Rudden



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.

Citation

Rudden, L. S., & Degiacomi, M. T. (2021). Transmembrane Protein Docking with JabberDock. Journal of Chemical Information and Modeling, 61(3), 1493-1499. https://doi.org/10.1021/acs.jcim.0c01315

Journal Article Type Article
Online Publication Date Feb 26, 2021
Publication Date 2021-03
Deposit Date Mar 20, 2021
Publicly Available Date Mar 28, 2024
Journal Journal of Chemical Information and Modeling
Print ISSN 1549-9596
Electronic ISSN 1549-960X
Publisher American Chemical Society
Peer Reviewed Peer Reviewed
Volume 61
Issue 3
Pages 1493-1499
DOI https://doi.org/10.1021/acs.jcim.0c01315
Public URL https://durham-repository.worktribe.com/output/1250746

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Copyright 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





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