Transmembrane Protein Docking with JabberDock.

Journal of Chemical Information and Modeling
Lucas S P Rudden, Matteo T Degiacomi

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.

References

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Aug 8, 2019·Journal of Chemical Theory and Computation·Lucas S P Rudden, Matteo T Degiacomi
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Jan 30, 2021·Chem·Anna OlerinyovaPhilipp Kukura

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Citations

Jun 18, 2021·Current Opinion in Structural Biology·Charlotte W van NoortAlexandre M J J Bonvin
Nov 18, 2021·The Protein Journal·Sharon Sunny, P B Jayaraj
Nov 19, 2021·Bioinformatics·Lucas S P RuddenMatteo T Degiacomi

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Software Mentioned

GROMACS
CAPRI
ZDOCK
STID
LightDock
PIPER
DOCK
Memdock
POW
KaR

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