I am trying to model a GPCR and I have a doubt about the transmembrane
It is known that they contain Pro residues which produce a kink in the
helix, so I am not interesting in modelling the seven helices as an
ideal helix .
My cuestions are:
1) If I do :
MAKE_RESTRAINTS RETRAINT_TYPE ='alpha'
Can MODELLER take account for these proline kinks ? (I mean if it has
specific backbone dihedarl angles for modelling them or should I
introduce them as constraints ?)
2) If not, is it a good option to divide the whole helix in segments,
excluding the prolines, and to force them to be an ideal alpha helix?
Thanks in advance.