ExTopoDB is a publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins.

Biochemical methods include: techniques of gene fusions, using enzymes such as alkaline phosphatase, ß-galactosidase, ß-lactamase, and various fluorescent proteins, detection of post-translational modifications such as glycosylation, phosphorylation and biotinylation, cysteine-scanning mutagenesis, proteolysis methods and epitope mapping techniques. The information is provided with references to the literature.

Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein's name and organism source.

The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB's protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction).

Tsaousis, G.N., Tsirigos, K.D., Andrianou, X.D., Liakopoulos, T.D., Bagos, P.G., Hamodrakas, S.J.
ExTopoDB: a database of experimentally derived topological models of transmembrane proteins.
Bioinformatics. 2010 Oct 1;26(19):2490-2.

Database statistics

Database version: 2.0 (Under update process)
Revision date: Jul 1, 2013
Total proteins: 2143
Organisms: 158

Contact information

Scientific questions: pbagosbiol.uoa.gr
Data submission: gtsaousisbiol.uoa.gr
Database administration: ktsirigbiol.uoa.gr

University of Athens
Faculty of Biology
Biophysics & Bioinformatics Laboratory