ArticleBioinformatics (Oxford, England)2020
MemBlob database and server for identifying transmembrane regions using cryo-EM maps.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- MPLID (Membrane Protein-Lipid Interaction Database): A Large-Scale Experimental Resource of Residue-Level Protein-Lipid Contacts.GigaScience · 2026Article
- Structural basis for calcium-stimulating pore formation of Vibrio α-hemolysin.Nature communications · 2023Article
- Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology.International journal of molecular sciences · 2022Article
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5 authors.
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Abstract
summaryThe identification of transmembrane helices in transmembrane proteins is crucial, not only to understand their mechanism of action but also to develop new therapies. While experimental data on the boundaries of membrane-embedded regions are sparse, this information is present in cryo-electron microscopy (cryo-EM) density maps and it has not been utilized yet for determining membrane regions. We developed a computational pipeline, where the inputs of a cryo-EM map, the corresponding atomistic structure, and the potential bilayer orientation determined by TMDET algorithm of a given protein result in an output defining the residues assigned to the bulk water phase, lipid interface and the lipid hydrophobic core. Based on this method, we built a database involving published cryo-EM protein structures and a server to be able to compute this data for newly obtained structures. AVAILABILITY AND IMPLEMENTATION: http://memblob.hegelab.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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