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[modeller_usage] Antibody Modelling
- To: modeller_usage-owner AT salilab.org, modeller_usage@listsrv.ucsf.edu
- Subject: [modeller_usage] Antibody Modelling
- From: "selva AT pnu.edu" <eselvakumar AT yahoo.com>
- Date: Mon, 4 Feb 2008 04:18:52 -0800 (PST)
- Reply-to: selva AT pnu.edu
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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