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