Re: [modeller_usage] Are gap in target and template same.

[Modeller Caretaker <>]

On 03/31/2011 09:27 PM, Ashish Runthala wrote:
> I am facing an interesting problem. Are gaps in target and template
> same, as shown below.
>
> Target     AAAAA       AA--A        AA--A
> Template    AA--A       AAAAA        AA--A
>            CaseI       CaseII       CaseIII
>
> Are these three cases I,II,&  III modelled the same way.

No. Case I is an insertion. The inserted region in the target (loop) 
will be modeled using just the CHARMM forcefield. Case II is a deletion 
- the template residues aligned with the deleted region won't be used. 
Case III is just a regular 1:1 alignment - since the gaps are in both 
target and template they are ignored.

> How will the gap penalties be incorporated in these three cases, when
> the modeller calculates the alignment score.

Modeller does not use gap penalties in the modeling process, nor does it 
calculate an alignment score.

	Ben Webb, Modeller Caretaker
--
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