Dear Modeller_usage members,
I have made 100 models of a ~260 residue protein (enzyme) using Modeller. The model has three loop regions which have significant deviation when compared with the template structure used for modelling. the first loop is due to an insertion in the model protein's sequence(i.e. this region of 3 residues is absent in the template sequence); second loop is a 16-residue long loop located at active site cleft (a region not resolved in template) ; third loop also doesn't have information from template but is a 4-residue loop.
I have the following doubts and questions: Do I need to refine all of these three loops? and should there be an order in which to refine each of these loops ( i mean, starting from N-terminus of the larger loop, etc)? Do small loops (1-5 residues) need to be refined only by the modeller script 'model-loop-tiny.py'? If yes, please explain, why? Or the regular 'loop.py' script is fine?
Thanks in advance, Vipul