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Bioinformatics Advance Access published online on April 23, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn202
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Gábor E. Tusnády 1,*, Lajos Kalmár 1, Hédi Hegyi , Péter Tompa and István Simon

Institue of Enzymology, BRC, Hungarian Academy of Sciences, H-1113 Karolina út 29, Budapest, Hungary.

*To whom correspondence should be addressed. Dr. Gábor E. Tusnády, E-mail: tusi{at}enzim.hu


  Abstract

Summary: 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{at}enzim.hu, lkamar{at}enzim.hu

Associate Editor: Prof. Burkhard Rost

1These authors contributed equally

Received on March 21, 2008; revised on April 14, 2008; accepted on April 21, 2008

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