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Re: [modeller_usage] Modelling T-cell Receptors

On 9/6/17 1:06 PM, Ryan Ehrlich wrote:
1.) How do I build a profile for multi-chain sequences?

You don't. These methods are designed to find single-chain templates, so one approach would be to search for templates for each chain individually, then combine all of the results into a multi-template alignment.

2.) I mentioned this in the first part, but I'd like to use multiple templates for this analysis. Do I used the PDB ID and each chain associated with the TCR, when doing so?

Not sure what you're asking here. Each template would need a unique name (align code) but you can call it whatever you want. Convention is to use PDB ID + chain ID, but you're not required to do that.

Also how should I modify the restraints argument between TCR chains?

What is the "restraints argument"?

3.) Accurate modeling of the CDR loops of the TCR (essentially the active site) is important to my research, should I use loopmodel() or other means for loop refinement?

This is probably a good idea.

	Ben Webb, Modeller Caretaker
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