Re: [modeller_usage] How can modeller build the structure of antibodies ?
To: jitrayut jitonnom <>
Subject: Re: [modeller_usage] How can modeller build the structure of antibodies ?
From: Modeller Caretaker <>
Date: Mon, 12 Mar 2007 13:00:14 -0700
Cc:
jitrayut jitonnom wrote:
I want to know that can modeller build some kind of antibodies structure
in which they have two chains (Vl and Vh). Actually, I have searched for
some similar problems but I am still in doubt. Besides, I also found the
literatures that use the modeller program to build the antibody model.
Most of them did not tell more details on how they performed to obtain
the antibody model. All I know from those papers are that there are two
ways to performs: first, model two chains from a single template;
second, model those two chains separately. Therefore, I was wondering
that which one is the best method and how to do modeling by using
modeller. Especially, after modeling the two chains (in case of the
second method) how can I concatenate these chains?
For the second method, you will need to add additional constraints or do
some additional modeling or docking simulations with the generated
models, since Modeller will not know the relative orientation of the two
chains.