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Re: [modeller_usage] Antibody Modelling

I have tried both way and end up with different problem.

1) By editing the non-loop regions in loop templates.
The resulted model contains a very strange loop region (the orientation of loop, which bends very high and leads to RMSD >5 for loop region backbone alone).
So I tried to fix this problem by increasing the flanking conserved regions of the loops.But still I am getting the same problem.

2) By listing the sequence in aligment file as per usual
Here I couldnot make the alingment for all four templates. Since the sequence length for one template is ~110 amino acids.

If I use the 2nd way by using the templates one by one keeping the each resulted model as myinitial model for modelling the next loop, Will it be a correct model ?

Please give me your valuable suggestions...

Selva

"selva AT pnu.edu" <eselvakumar AT yahoo.com> wrote:
I want to model an antibody structure with multiple templates for specific segments from each template based on the below alignment for two chains seperately. Since I know the domain interface residues, I could able to superimpose their relative orientation after modelling seperately.
 
L-CHAIN TARGET__: AAAAAAAAAA11111AAAAAAAAAA22222AAAAAAAAAA33333AAAAAAAAAA
L-CHAIN TEMPLATE: AAAAAAAAAAxxxxxAAAAAAAAAAxxxxxAAAAAAAAAAxxxxxAAAAAAAAAA
LOOP-L1 TEMPLATE: xxxxxxxxxx11111xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-L2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx22222xxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-L3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx33333xxxxxxxxxx
 
 
H-CHAIN TARGET__: BBBBBBBBBB44444BBBBBBBBBB55555BBBBBBBBBB66666BBBBBBBBBB
H-CHAIN TEMPLATE: BBBBBBBBBBxxxxxBBBBBBBBBBxxxxxBBBBBBBBBBxxxxxBBBBBBBBBB
LOOP-H1 TEMPLATE: xxxxxxxxxx44444xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-H2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx55555xxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-H3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx66666xxxxxxxxxx
 
 
I wish to know how to specify the segment positions to be modeled from each template or
 
Is there anyother easy way of modelling the same?.
 
Selva
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