TOPDOM is a collection of domains and sequence motifs located conservatively in one side of transmembrane proteins. The database was created by scanning well annotated transmembrane protein sequence in UniProt database 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 inUniProt database. Transmembrane proteins subset of UniProt were scanned by using hmmpfam algoritm withPfam and Smart domain databases, prosite scan with Prosite motif database and fingerprints algorithm with Prints database. TOPDOM can be downloaded either the whole database or various subset of the database in XML format. The database can be searched bykeywords or identifiers. Moreover, users can scan their protein sequences agains the TOPDOM domains and motifs. Constrained prediction can be performed after sequence scanning by theHMMTOP transmembrane topology prediction algorithm using the search results as constrains.
The Topology Data Bank of Transmembrane Proteins (TOPDB) is currently the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information. The database collects the details of various experiments carried out to learn about the topology of particular transmembrane proteins. The experimental techniques include fusion with reporter enzymes, glycolysation studies, protease accessibility, immunolocalisation, etc. In addition to literature-derived data, an extensive collection of structural data was also compiled from Protein Data Bank (PDB) and from Protein Data Bank of Transmembrane Proteins (PDBTM) by utilising the TMDET algorithm.
PDBTM is the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB). The database was created by scanning all PDB entries with TMDET algorithm. You can read more about PDBTM in our articles and in PDBTM manual.