TOPDOM: database of domains and motifs with conservative location in transmembrane proteins

Bioinformatics. 2008 Jun 15;24(12):1469-70. doi: 10.1093/bioinformatics/btn202. Epub 2008 Apr 23.


The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in alpha-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or motif detecting algorithms. The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database. The information about the location of the collected domains and motifs can be incorporated into constrained topology prediction algorithms, like HMMTOP, increasing the prediction accuracy.

Availability: The TOPDOM database and the constrained HMMTOP prediction server are available on the page


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Conserved Sequence
  • Database Management Systems*
  • Databases, Protein*
  • Information Storage and Retrieval / methods*
  • Membrane Proteins / chemistry*
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • User-Computer Interface*


  • Membrane Proteins