Memdock: An α-helical membrane protein docking algorithm

Naama Hurwitz*, DIna Schneidman-Duhovny, Haim J. Wolfson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

33 Scopus citations

Abstract

Motivation: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR spectroscopy analyses. All the more so, there is only a small number of membrane protein-protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial. Numerous methods for docking globular proteins exist, however few have been developed especially for membrane proteins and designed to address docking within the lipid bilayer environment. Results: We present a novel algorithm, Memdock, for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment for docking as well as for refining and ranking the docking candidates. We show that our algorithm improves both the docking accuracy and the candidates ranking compared to a standard protein-protein docking algorithm.

Original languageEnglish
Pages (from-to)2444-2450
Number of pages7
JournalBioinformatics
Volume32
Issue number16
DOIs
StatePublished - 15 Aug 2016

Funding

FundersFunder number
Hermann Minkowski Minerva Geometry Center
Israel Science Foundation1112/12
Israeli Centers for Research Excellence1775/12

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