MembraneFold: Visualising transmembrane protein structure and topology

Background AlphaFold’s accuracy, which is often comparable to that of experimentally determined structures, has revolutionized protein structure research. Being a statistical method, AlphaFold implicitly infers the cellular environment, e.g. the cell membrane, from the protein sequence. Membrane protein topology prediction methods predict the cellular environment for each protein residue but not the structure. Current structure and topology tools thus provide complementary information. Results We introduce the web server MembraneFold. MembraneFold combines protein structure (from an uploaded PDB file/AlphaFold DB/OmegaFold) and topology (DeepTMHMM) prediction in one server. The output is shown both as a structure with topology superimposed and as a sequence annotation. MembraneFold uses structures predicted by OmegaFold if neither a PDB file is uploaded nor the structure is available in AlphaFold DB. Conclusion MembraneFold is a user-friendly web server that provides practitioners with fast and accurate information about membrane proteins. It is available at https://ku.biolib.com/MembraneFold/.