TMbed
Transmembrane protein and topology prediction at residue level.
Summary
- Model name:
TMbed - Task: Prediction of transmembrane proteins and topology
- Protocol:
residue_to_class - Embedder:
Rostlab/prot_t5_xl_uniref50 - Model size:
1.4 MB
Outputs
trans_membrane
- Description: Per-residue transmembrane topology prediction
- Output type:
per_residue - Value type:
str
| Shortcut | Label | Meaning |
|---|---|---|
B | Transmembrane beta strand | Residue is part of a transmembrane beta strand (IN → OUT orientation) |
b | Transmembrane beta strand | Residue is part of a transmembrane beta strand (OUT → IN orientation) |
H | Transmembrane alpha helix | Residue is part of a transmembrane helix (IN → OUT orientation) |
h | Transmembrane alpha helix | Residue is part of a transmembrane helix (OUT → IN orientation) |
S | Signal peptide | Residue is part of a signal peptide |
i | Non-transmembrane, inside | Residue is on the cytoplasmic side |
o | Non-transmembrane, outside | Residue is on the extracellular side |
References
- Authors: Bernhofer, Michael; Rost, Burkhard
- Model link: github.com/BernhoferM/TMbed
- Citation: doi.org/10.1186/s12859-022-04873-x
- License:
Apache-2.0 - Training data: data.bioembeddings.com/public/design