Determining what transmembrane predictor works best is quite
difficult, as there is very little solid experimental data determining
transmembrane regions---most of the transmembrane regions are known
only as a result of homology to other proteins or by prediction with
one of the methods. Determining who has the most reliable results is
difficult when most of the "known answers" are just someone else's
predictions.
If you use several different transmembrane predictors that use
different methods, and they all give you the same transmembrane
helices, then you can be pretty sure of them---the signal is quite strong.
When some predict transmembrane helices and some do not, then some
experimental evidence should be obtained before you put too much
believe in the predictions.
One can reasonably expect that predictors that use multiple alignments
are more likely to be accurate than predictors that use only a single
sequence, based on the experience of 2ry structure prediction of
globular proteins. The lack of good large test sets makes even this an
untested conjecture.
(Note: if someone has put together a large, experimentally verified
set of transmembrane helices, I'd be interested in hearing about it.
Maybe then I'd try making a transmembrane helix predictor.)
--
Kevin Karplus karplus at cse.ucsc.eduhttp://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck
Anything below this line is junk added by others without my approval.
