Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models

The Membranome database provides comprehensive structural information on single-pass (i.e., bitopic) membrane proteins from six evolutionarily distant organisms, including protein-protein interactions, complexes, mutations, experimental structures, and models of transmembrane α-helical dimers. We present a new version of this database, Membranome 3.0, which was significantly updated by revising the set of 5,758 bitopic proteins and incorporating models generated by AlphaFold 2 in the database. The AlphaFold models were parsed into structural domains located at the different membrane sides, modified to exclude low-confidence unstructured terminal regions and signal sequences, validated through comparison with available experimental structures, and positioned with respect to membrane boundaries. Membranome 3.0 was re-developed to facilitate visualization and comparative analysis of multiple 3D structures of proteins that belong to a specified family, complex, biological pathway, or membrane type. New tools for advanced search and analysis of proteins, their interactions, complexes, and mutations were included. The database is freely accessible at https://membranome.org.