In article <4486ld$dpu at news.ust.hk>, bclong at uxmail.ust.hk (Terence) wrote:
>> I often read in journals that a certain transmembrane topology is
>determined/predicted for a certain transmemnrane protein. How is this done?
>Is this done thru some commercial/public domain software? Or is it just by
>eyeballing how many hydrophobic segment there?
There are a number of transmembrane topology prediction algorithms, none of
which is very reliable - for a review see Fasman & Gilbert, TIBS 15 (1990),
pp. 89-92 and a contradicting opinion in the same TIBS issue by Jaehnig, TIBS
15 (1990), pp. 93-95. You will find citations for the algorithms in the first
paper. Generally speaking, results for the prediction of transmembrane
peptides are difficult to assess since there are only few crystal structures
available for these domains. Hope this helps, check out the two papers.