The present version is able to predict topologies from eukaryotic and prokaryotic proteins. It calculates:

1) The hydrophobicity profile according with the trapezoid algorithm.

2) The transmembrane segments: TopPred finds all the peaks above an upper cutoff that qualify as certain transmembrane segments, as well as those peaks above a lower cutoff that qualify as putative ones. In the current version, three different algorithms can be used to search the transmembrane domains.

3) The possible topologies: TopPred generates the topologies including all certain ones, and either including or excluding the putative transmembrane segments, calculating different distribution parameters for each topology.

A more detailed description of calculations and parameters can be found in:

• Claros & von Heijne (1994) Comput. Applic. Biosci. 10:685-686 [about the software]
• von Heijne (1992) J. Mol. Biol. 255:487-494  [about (1) and (2)] 
• Sipos & von Heijne (1993) Eur. J. Biochem. 213:1333-1340   [about (3)]