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

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  • Additional Information
    • Source:
      Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE
    • Publication Information:
      Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press
      Original Publication: New York, N.Y. : Cambridge University Press, c1992-
    • Subject Terms:
      Membrane Proteins*/chemistry ; Membrane Proteins*/genetics; Databases, Protein ; Protein Conformation, alpha-Helical
    • Abstract:
      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.
      (© 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)
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    • Contributed Indexing:
      Keywords: full-length protein model; network analysis; visualization; web tool
    • Accession Number:
      0 (Membrane Proteins)
    • Publication Date:
      Date Created: 20220428 Date Completed: 20220502 Latest Revision: 20220716
    • Publication Date:
      20240104
    • Accession Number:
      PMC9047035
    • Accession Number:
      10.1002/pro.4318
    • Accession Number:
      35481632