AlphaPPM places AlphaFold models of single-pass membrane proteins into the bilayer
- AlphaPPM is a pipeline and web server that spots single-pass membrane proteins among AlphaFold models. It trims low-confidence regions and signal sequences, splits domains, then orients them against the membrane using the PPM and FMAP approaches.
- It was applied to complete bitopic protein sets from 18 organisms, with manual curation and cross-validation.
- The resulting MembranomeX resource holds roughly 17,000 oriented models grouped into functional classes and families, plus complex data, and includes bitopic proteins missing from existing databases.
💡 Points Based on the abstract
Single-pass proteins are usually the awkward cases in membrane docking and MD setup, because the tilt and hydrophobic thickness you assume for the bilayer decide whether the extracellular domain is even sensible. I'd want to see how oriented models compare with experimental or OPM entries before trusting them. Also, AlphaFold gives one static conformation, so check receptor-type targets whose ligand-bound state may differ.
📄 Paper · Journal of Chemical Information and Modeling (ACS) ↗ Proteome-Wide Identification and Membrane Positioning of Single-Pass Membrane Proteins Using AlphaFold Models