[modeller_usage] Modelling of the interface of a protein complex

[Karsten SUHRE <>]

Dear Modeller users,

To study the interface between two proteins in complex
(A+B), i.e. to decide whether these proteins may form a complex, I wish to 
compute a homology model on the basis of an existing, but only remotely 
homologous, complex (A'+B'), i.e. there are difference in some indels close 
to the interface.

Each of the target proteins has also a closely homologous template, (A" and 
B"), which I would like to use to model the indels.

However, as I am particularly interested in the interface, it is crucial to 
model the sidechains at the interface correctly, that is to account for the 
presence of the binding partner. Thus, the remote homologue (A+B) bears some 
important information as what concerns the complex.

The most direct approach would be to use all templates and let MODELLER decide 
what to do. But is this really the optimal approach?

Thank you very much in advance for any suggestion, or reference to similar 
problems.

Kind regards,

Karsten.