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

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

Author information

1
Institue of Enzymology, BRC, Hungarian Academy of Sciences, H-1113 Karolina út 29, Budapest, Hungary. tusi@enzim.hu

Abstract

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.hu

CONTACT:

tusi@enzim.hu; lkalmar@enzim.hu.

PMID:
18434342
PMCID:
PMC2427164
DOI:
10.1093/bioinformatics/btn202
[Indexed for MEDLINE]
Free PMC Article

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