I would like to pose a question. I am doing homology modeling of various
proteins, some of which are
really straightforward to model, others, due to some issues, not.
I have a problem in this case: a protein has one or several folded
domains and long, unstructured parts that
are connecting them. Sometimes on those unstructured parts are very
small folded parts, sometimes not.
What is critical for me is to model these unstructured parts as close to
the original template as possible.
Instead, I land up with models with these loops that are going all ways
but the way it was in the template.
This happens also in the situation when two sequences have really high
identities and similar lengths.
Is there a way to tell Modeller to model these parts as close to the
model as possible?