[modeller_usage] error with loops in transmembrane receptor model

["Vasillis Myrianthopoulos" <>]

Hi everybody,

I am trying to build a model of a transmembrane receptor and I get serious
problems and obvious steric errors on the loops which connect the TM
helices. The alignment is correct on a biological and phylogenetic basis
however there are large insertions on the loops. As a result, there are
two main errors that appear in the model. First, the loops are modelled as
packed between the TM helices and not as free moving segments that can
float in the solvent environment and second, in some cases the loops form
kind of knots which are obviously wrong. I guess that there must be some
kind of parameter within MODELLER that directs the construction towards
the maximum intramolecular contact, this is the only way I can explain
this wrong output. Does anybody have an idea on the matter?

many thanks,

Vassilis