Abstract
Memdock is a tool for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment. Given two α-helical membrane located protein molecules, the method outputs a list of potential complexes sorted by energy criteria. The program includes three steps: docking, refinement, and re-ranking of the results. All three docking steps have been customized to the membrane environment in order to improve performance and reduce program run-time. In this chapter, we describe the application of our web server, referred to as Memdock, for prediction of the docking complex for a pair of input membrane protein structures. Memdock is freely available for academic users without registration at http://bioinfo3d.cs.tau.ac.il/Memdock/index.html.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Jones DT (1998) Do transmembrane protein superfolds exist? FEBS Lett 423(3):281–285. https://doi.org/10.1016/S0014-5793(98)00095-7
Wallin E, Heijne GV (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7(4):1029–1038. https://doi.org/10.1002/pro.5560070420
Yıldırım MA, Goh KI, Cusick ME et al (2007) Drug—target network. Nat Biotechnol 25(10):1119–1126. https://doi.org/10.1038/nbt1338
Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank. Nucleic Acids Res 28(1):235–242. https://doi.org/10.1093/nar/28.1.235
Carpenter EP, Beis K, Cameron AD, Iwata S (2008) Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 18(5):581–586. https://doi.org/10.1016/j.sbi.2008.07.001
Duhovny D, Nussinov R, Wolfson HJ (2002) Efficient unbound docking of rigid molecules. In: Guigó R, Gusfield D (eds) Algorithms in bioinformatics. WABI 2002, Lecture notes in computer science, vol 2452. Springer, Berlin, pp 185–200. https://doi.org/10.1007/3-540-45784-4_14
Mashiach E, Nussinov R, Wolfson HJ (2010) FiberDock: flexible induced-fit backbone refinement in molecular docking. Proteins 78(6):1503–1519. https://doi.org/10.1002/prot.22668
Hurwitz N, Schneidman-Duhovny D, Wolfson HJ (2016) Memdock: an α-helical membrane protein docking algorithm. Bioinformatics 32(16):2444–2450. https://doi.org/10.1093/bioinformatics/btw184
Lomize MA, Pogozheva ID, Joo H et al (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res 40(Database issue):D370–D376. https://doi.org/10.1093/nar/gkr703
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Hurwitz, N., Wolfson, H.J. (2021). Memdock: An α-Helical Membrane Protein Docking Algorithm. In: Moreira, I.S., Machuqueiro, M., Mourão, J. (eds) Computational Design of Membrane Proteins. Methods in Molecular Biology, vol 2315. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1468-6_7
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1468-6_7
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1467-9
Online ISBN: 978-1-0716-1468-6
eBook Packages: Springer Protocols