Provides spatial positions of membrane-bound peptides and proteins of known 3D structure in the lipid bilayer. OPM is a curated web resource which contains more than 1200 transmembrane and peripheral proteins and peptides from approximately 350 organisms that represent approximately 3800 Protein Data Bank (PDB) entries. The database also indicates structural classification, topology and intracellular localization.
A collection of domains and sequence motifs located conservatively in one side of membranes either in transmembrane or globular proteins. TOPDOM was created by predicting the transmembrane status and topology of all protein sequence in UniProt database by the CCTOP algorithm and scanning by specific domain or motif detecting algorithms. The identified domain or motif was added to the database if it was uniformly annotated in the same side of the membrane of the various proteins in UniProt database.
A comprehensive database of helical membrane proteins featuring internal atomic packing densities, internal cavities and internal waters. MP:PD encloses all alpha helical transmembrane proteins derived from the OPM database, PDBTM, or MPstruc. MP:PD is thus a sub dataset of the wwPDB and lists only proteins with at least one transmembrane helix.
Collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable. Motifs contained in MeMotif can be used in different biological applications, from the identification of biochemically important functional residues which are candidates for mutagenesis experiments to the improvement of tools for transmembrane protein modeling.
This database is a compilation of the predictions made by the Freeman-Wimley algorithm, which was shown to be among the most accurate predictor of TMBBs. Also included are N-terminal export signal peptide predictions made by the SignalP server.
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