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?

See http://salilab.org/modeller/9v1/manual/node27.html

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.

Ben Webb, Modeller Caretaker