About TMVisDB

TMVisDB provides per-residue transmembrane topology annotations for proteins predicted as transmembrane proteins from the AlphaFold DB. The annotations are predicted with TMbed, and are visualized by overlaying them with AlphaFold 2 structures.

Overview of TMVisDB

How to browse TMVisDB:

To browse the 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

Note: We follow the general length restrictions of AlphaFold DB: a minimum of 16 amino acids for all organisms, and a maximum of 1,280 amino acids for all organisms except SwissProt (2,700 amino acids) and human (no restrictions).

How to visualize predicted transmembrane proteins:

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 are 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.

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