Database used/linked

Topology data for the constrained prediction methods is collected from three different resources. The most reliable data can be found in the PDBTM database, which contains the 3D structure of transmembrane proteins together with the most likely membrane orientation determined by the TMDET algorithm. Since PDBTM contains only topography, i.e. the sequential localization of the transmembrane helices.

This information is extended by using the experimentally established topology data of transmembrane proteins from TOPDB database, which was updated recently from several resources and contains 75.211 topology data from more than four thousand (4.910) transmembrane proteins. 

The third resource is TOPDOM, which is a collection of domains and sequence motifs located conservatively in the cytosolic or extra-cytosolic side of transmembrane proteins. We use the search engine of TOPDOM homepage to locate these domains/motifs in the human sequences and we used the position and topology localization of the result(s) as constraint(s).


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