A membrane protein complex docking benchmark
Open accessAbstract
We report the first membrane protein-protein docking benchmark consisting of 37 targets of diverse functions and folds. The structures were chosen based on a set of parameters such as the availability of unbound structures, the modeling difficulty and their uniqueness. They have been cleaned and consistently numbered to facilitate their use in docking. Using this benchmark, we establish the baseline performance of HADDOCK, without any specific optimization for membrane proteins, for two scenarios: true interface-driven docking and ab initio docking. Despite the fact that HADDOCK has been developed for soluble complexes, it shows promising docking performance for membrane systems, but there is clearly room for further optimization. The resulting set of docking decoys, together with analysis scripts, is made freely available. These can serve as a basis for the optimization of membrane complex-specific scoring functions.
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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 [17]
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References 31 · Cited by 23
- Authors
- Koukos, P. I., Faro, I., van Noort, C. W., & Bonvin, A. M. J. J.
- Affiliations
- Utrecht University (NL)
- Corresponding author
- Bonvin, Alexandre M.J.J.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2018-12
- Volume
- 430
- Issue
- 24
- Pages
- 5246-5256
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2899758436
- Cited by
- 23
- References
- 31
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 2 · 2023: 1 · 2022: 2 · 2021: 6 · 2020: 4 · 2019: 5
- FWCI
- 1.33
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Molecular Biology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- European H2020 e-Infrastructure (675858)
- BioExcel (675728)
- Dutch Foundation for Scientific Research (718.015.001)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- membrane proteins, protein-protein docking, docking benchmark, haddock, scoring functions, membrane protein complexes
- MeSH terms
- Membrane Proteins, Models, Molecular, Computational Biology, Benchmarking, Protein Interaction Mapping, Molecular Docking Simulation
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