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:
*AAAAAAAAAA*xxxxx*AAAAAAAAAA*xxxxx*AAAAAAAAAA*xxxxx*AAAAAAAAAA*
LOOP-L1 TEMPLATE: xxxxxxxxxx*11111*xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-L2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx*22222*xxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-L3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*33333*xxxxxxxxxx
H-CHAIN TARGET__: *BBBBBBBBBB44444BBBBBBBBBB55555BBBBBBBBBB66666BBBBBBBBBB*
H-CHAIN TEMPLATE:
*BBBBBBBBBB*xxxxx*BBBBBBBBBB*xxxxx*BBBBBBBBBB*xxxxx*BBBBBBBBBB*
LOOP-H1 TEMPLATE: xxxxxxxxxx*44444*xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-H2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx*55555*xxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-H3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*66666*xxxxxxxxxx
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?.