Memdock: an α-helical membrane protein docking algorithm
Open accessAbstract
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. AVAILABILITY AND IMPLEMENTATION: http://bioinfo3d.cs.tau.ac.il/Memdock/ CONTACTS: namih@tau.ac.il or wolfson@tau.ac.il SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Other types of molecules interacting with proteins, as well as protein-protein interactions in membranes, have been studied extensively through the years.
“While other types of molecules interacting with proteins, as well as protein-protein interactions in membranes, have been studied extensively through the years [14–18]”
From Challenges in protein docking (2020) · cites this paper as [16]
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- Authors
- Hurwitz, N., Schneidman-Duhovny, D., & Wolfson, H. J.
- Affiliations
- Tel Aviv University (IL)
- 2 Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Corresponding author
- Hurwitz, Naama
- Wolfson, Haim J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-04-08
- Volume
- 32
- Issue
- 16
- Pages
- 2444-2450
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2320663134
- Cited by
- 40
- References
- 41
- Citations by year
- 2025: 2 · 2024: 3 · 2023: 3 · 2022: 6 · 2021: 10 · 2020: 7 · 2019: 4 · 2018: 3 · 2017: 2
- FWCI
- 1.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Israeli Centers for Research Excellence (1775/12)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- alpha-helical membrane proteins, protein-protein docking
- MeSH terms
- Algorithms, Membrane Proteins, Models, Molecular, Databases, Protein
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