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[modeller_usage] from ylwang: loop conformation sampling

Dear modeller,

Firt, thanks for Ben Webb's help on my question, I follow your advice and found that error in MASS line.

Now, I want to ask questioins about loop conformation.
A loop in involved in the ligand binding and also involved in the dimmer interface. In the templet, the loop is short, but for my protein, it is longer than templet by 12 residues. The protein can be monomer or dimmer, but only be funcational in dimmer form. So, I want study:
1:  the impact of dimmer on the loop conformation.
2:  the impact of ligand on the loop conformation.

Can I do loop-refine process times for dimmer and monomer to the study 1 issue 1?
And Can I do modeller by "modeling ligands in the binding site" to study the issue 2?
Or, is there other ways for my issue.
I had read some paper about "ligand-supported homology model", but can't understand it well. It seems a method, but no tool-package availble?
Any advices, please!

PH.D Student
Shanghai Key Lab. of Chemical Biology
School of Pharmacy
East China University of Science and Technology