biostudies-literatureLomize ALDivision of Biological InfrastructureNational Science Foundation of Sri Lankae4318https://www.ebi.ac.uk/biostudies/studies/S-EPMC9047035biostudies-literatureUnknown31(5)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 boundarProtein science : a publication of the Protein SocietyMembranome 3.0: Database of single-pass membrane proteins with AlphaFold models.PMC90470351855425Todd SCOuteiral CPogozheva IDDeane CMCherepanov SSchnitzer KALomize ALfalseMembranome 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 boundar2022-01-01T00:00:00Z2022 May2025-04-04T21:33:15.698Z2025-04-04T21:33:15.698ZS-EPMC90470353548163210.1002/pro.4318