ArticleNucleic acids research2023
TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed.
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- The nuclear envelope protein TMEM209 is an integral component of the nuclear pore complex and interacts with Nup210.Journal of cell science · 2026Article
- Membrane Protein Folding and Biogenesis: Insights from Single-Molecule Force Spectroscopy.Chemical reviews · 2026Review
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- Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.bioRxiv : the preprint server for biology · 2026Article
- PEX11 mediates intralumenal vesicle formation in peroxisomes.Nature communications · 2026Article
- Tmn blocks phage spread via plasmolysis and triggers synergistic defence responses.bioRxiv : the preprint server for biology · 2026Article
- Transmembrane proteins mediate basal complex assembly and individual daughter cell formation in malaria parasites.Science advances · 2026Article
- NanoporeDB: a structural resource of multimeric protein nanopores for single-molecule sensing.GigaScience · 2026Article
- MetaMP Ecosystem for Unified, Auditable, and Benchmark-Ready Data for Reliable Membrane Protein Annotation.Computational and structural biotechnology journal · 2026Article
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
- Genetic Diversity, Predictive Protein Structures, and Interaction Networks of Cysteine-Rich Receptor-Like Kinases inComputational and structural biotechnology journal · 2026Article
- Sterol-C4-methyl-oxidase Erg251 governs Candida albicans hypoxic growth, commensalism and virulence.Nature communications · 2025Article
- AGPAT2 acts at the crossroads of lipid biosynthesis and DRP1-mediated ER morphogenesis.Nature communications · 2025Article
- A novel DCSTAMP antagonist impedes preosteoclast fusion via modulation of RAP1B-RAC1-mediated cytoskeletal remodeling.Experimental & molecular medicine · 2025Article
- Deep learning-assisted tools to understand the structural biology of the synapse.Biomedical engineering letters · 2025Review
- Physics-based evolution of transmembrane helices reveals mechanisms of cholesterol attraction.Nature communications · 2025Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
AI-driven protein structure prediction, most notably AlphaFold2 (AF2) opens new frontiers for almost all fields of structural biology. As traditional structure prediction methods for transmembrane proteins were both complicated and error prone, AF2 is a great help to the community. Complementing the relatively meager number of experimental structures, AF2 provides 3D predictions for thousands of new alpha-helical membrane proteins. However, the lack of reliable structural templates and the fact that AF2 was not trained to handle phase boundaries also necessitates a delicate assessment of structural correctness. In our new database, Transmembrane AlphaFold database (TmAlphaFold database), we apply TMDET, a simple geometry-based method to visualize the likeliest position of the membrane plane. In addition, we calculate several parameters to evaluate the location of the protein into the membrane. This also allows TmAlphaFold database to show whether the predicted 3D structure is realistic or not. The TmAlphaFold database is available at https://tmalphafold.ttk.hu/.
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