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Re: [modeller_usage] from ylwang: loop conformation sampling

Wang Yanli wrote:
> 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!

When you perform loop modeling, the loop will "see" the rest of the
protein (in both the monomer and dimer cases) so you can certainly study
issue (1). For ligands, it is more complicated, since Modeller does not
know the specific interactions (e.g. electrostatics, or covalent bonds)
between the ligand and your loop. You would have to experiment and
perhaps add your own ligand-loop restraints by hand.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage