Good day, Modellers!
I'm a student and not yet rather familiar with Modeller. I've faced
some difficulties when modeling long loops. My target sequences are 35
residues long and have just slight differences (approximately five
residues) from the template. The only restraint to the models is a
disulfide bond connecting the first and the last residues. Several
known structures (completely different) are used as templates; the
result of the modeling each time are structures similar to the one
used as template. The structures are supposed to be variable: nothing
is known about their preferable conformation. Also there is no
suggestion of elements with definite secondary structure.
1) whether it is possible somehow to obtain a set of possible
conformations (not only those similar to the initial ones) by making
changes in initial conditions or with the help of any other means?
2) can the tools for loop modeling be applied here, because the length
of the loop seems to be excessive. Taking into account the low
accuracy of the models obtained is it then possible using some
assessment method (DOPE for example) to pick out more reliable models?
3) does the DOPE assessment method have any limitations on the minimal
length of the structure and how does its accuracy change with length
if it does?
Thank you a lot for any help.
Ivan