TOPDOM: Conservatively Located Domains and Motifs in Transmembrane Proteins

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 in UniProt database. Transmembrane proteins subset of UniProt were scanned by using hmmpfam algoritm with Pfam and Smart domain databases, prosite scan with Prosite motif database and fingerprints algorithm with Prints database. For further details refer to our manuscripts.

TOPDOM can be

    downloaded either the whole database or various subset of the database in XML format. The database can be searched by keywords or identifiers. Moreover, users can scan their protein sequences agains the TOPDOM domains and motifs.

Constrained prediction

    can be performed after sequence scanning by the HMMTOP transmembrane topology prediction algorithm using the search results as constrains.