Welcome to TMvisDB: A database to search and visualize predicted transmembrane proteins. 🦭
TMvisDB provides per-residue transmembrane topology annotations for all proteins in AlphaFold DB (~ 200 million proteins, September '22) predicted as transmembrane proteins (~ 46 million). The annotations are predicted with TMbed, and are visualized by overlaying them with AlphaFold 2 structures.
The web interface of TMvisDB is implemented with Streamlit, and accessible here: https://tmvisdb.predictprotein.org.
Figure caption
3D structure and membrane topology visualization protein DnaJ homolog subfamily C member 11 (Q9NVH1). The protein DnaJ with (A) per-residue topology color-scheme: inside-to-outside TMH (light green), outside-to-inside TMH (dark green), inside-to-outside TMB (light blue), outside-to-inside TMB (dark blue), signal peptide (pink), other (grey), and (B) a per-residue AlphaFold color-scheme based on the confidence measure predicted local distance test (pLDDT): very low pLDDT ≤ 50 (red), low 50 < pLDDT ≤ 70 (yellow), confident 70 < pLDDT ≤ 90 (green), very confident pLDDT > 90 (blue). The predicted transmembrane topology aligns well with the predicted AlphaFold structure in regions of high pLDDT, and the length of the alpha-helix and beta-barrel could align with membrane boundaries.
To browse the 46 million predicted transmembrane proteins in TMvisDB via a table, you can show a random selection or use the following filters:
- Transmembrane topology (alpha-helix, beta-strand)
- Include/Exclude sequences with predicted signal peptides
- Taxonomy (UniProt Organism Identifier, Domain, Kingdom)
- Protein length
Single proteins of TMvisDB can be selected for 3D-visualization of per-residue transmembrane topology annotation. You can either select a protein from the table you generated while browsing TMvisDB, or you can directly enter a UniProt Identifier. The AlphaFold 2 structures of a protein is then shown with the corresponding color code of the predicted topology. You may also select the pLDDT score of AlphaFold 2 as a color code.
- Preprint for TMvisDB: TMvisDB
- Structure predictions: Alphafold DB
- Transmembrane topology predictions: TMbed
- Visualization: TMvis
- Protein-specific phenotype predictions: LambdaPP
- Structural aligments: Foldseek
- Corresponding Author: Céline Marquet
- License: License
- Resources & Maintenance: Rostlab