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