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

TitleTOPDOM: database of domains and motifs with conservative location in transmembrane proteins.
Publication TypeJournal Article
Year of Publication2008
AuthorsTusnády, G. E., L. Kalmar, H. Hegyi, P. Tompa, and I. Simon
JournalBioinformatics
Volume24
Issue12
Pagination1469-70
Date Published2008 Jun 15
ISSN1367-4811
KeywordsAlgorithms, Amino Acid Motifs, Amino Acid Sequence, Conserved Sequence, Database Management Systems, Databases, Protein, Information Storage and Retrieval, Membrane Proteins, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment, Sequence Analysis, Protein, User-Computer Interface
Abstract

UNLABELLED: 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 http://topdom.enzim.huCONTACT: tusi@enzim.hu; lkalmar@enzim.hu.

DOI10.1093/bioinformatics/btn202
Alternate JournalBioinformatics
PubMed ID18434342
PubMed Central IDPMC2427164
Grant ListISRF GR067595 / / Wellcome Trust / United Kingdom