On 9/14/10 4:15 PM, Darren Leneghan wrote: > I'm trying to generate a model which uses the crystal structure of a > homologous protein which is in complex with its interacting partners in > a small complex. The crystal structure PDB files for the individual > parts of the complex, as well as for the whole complex are available. > How would I go about substituting my protein into the model?

If I understand you correctly, you want to produce a complex with a single component replaced with its modeled homolog. There are two ways you can achieve this:

1. Build a model of the protein using just the homologous protein from the complex. Then superpose the model on the template (to get them in the same frame of reference) and combine the model PDB file with the complex PDB file, either manually (in a text editor) or with a viewer such as Chimera.

2. Build a model of the entire complex using an alignment such as:

>P1;template structureX:1abc:1:A:10:C:::: AAAAAAAAAA/BBBBBBBBBB/CCCCCCCCCC*

>P1;target sequence:::::::: AAAAAAAAAA/bbbbbbbbbb/CCCCCCCCCC*

Here I'm assuming that your template complex, 1abc, contains three chains, of which the B chain is the homologous protein. Then your model (target) will also contain three chains, the B chain being the protein you want to model and the A and C chains being 100% identical to the template. The A and C chains may move during the modeling procedure, however - if you don't want this you can select just the B chain for refinement with a script similar to that at http://salilab.org/modeller/9v8/manual/node23.html

Ben Webb, Modeller Caretaker