ArticleBMC bioinformatics2013
Membrane protein orientation and refinement using a knowledge-based statistical potential.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 107 citations in OpenAlex.
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- MemPrO: A Predictive Tool for Membrane Protein Orientation.Journal of chemical theory and computation · 2026Article
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- Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove.eLife · 2025Article
- TmDet 4.0: determining membrane orientation of transmembrane proteins from 3D structure.Nucleic acids research · 2025Article
- SpoIIIL is a forespore factor required for efficient cell-cell signalling during Bacillus subtilis sporulation.PLoS genetics · 2025Article
- Conformational dynamics and membrane insertion mechanism of B4GALNT1 in ganglioside synthesis.Nature communications · 2025Article
- CD9 knockdown inhibits cell proliferation, migration, and invasion and augments apoptosis in tongue cancer cells through regulation of the EGFR signalling pathway.Molecular biology reports · 2025Article
- Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove.bioRxiv : the preprint server for biology · 2025Article
- N-Branched Tricyclic Guanidines as Novel Melanocortin-3 Receptor Agonists and Melanocortin-4 Receptor Antagonists.Journal of medicinal chemistry · 2025Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundRecent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. Identifying the correct orientation allows us to study the complex relationship between sequence, structure and the lipid environment, which is otherwise challenging to investigate using experimental techniques due to the difficulty in crystallising membrane proteins embedded within intact membranes.
resultsWe have developed a knowledge-based membrane potential, calculated by the statistical analysis of transmembrane protein structures, coupled with a combination of genetic and direct search algorithms, and demonstrate its use in positioning proteins in membranes, refinement of membrane protein models and in decoy discrimination.
conclusionsOur method is able to quickly and accurately orientate both alpha-helical and beta-barrel membrane proteins within the lipid bilayer, showing closer agreement with experimentally determined values than existing approaches. We also demonstrate both consistent and significant refinement of membrane protein models and the effective discrimination between native and decoy structures. Source code is available under an open source license from http://bioinf.cs.ucl.ac.uk/downloads/memembed/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.