Hi,
I'm trying to create a homology model incorporating bound substrate. Can I do this with I-Tasser? I noticed in the output of your models there is a section entitled "Predicted Binding Site." This appears to have what I'm looking for - there are links to models which include the sequence I submitted with bound substrate, but I wanted to verify these are valid for analysis.
It's a little confusing because I've submitted sequence for two different paralogs to a number of modeling servers. For the most part, the RMSD when I compare the models is low 0.02 to 0.20 A. The I-Tasser numbers are closer to 0.75. Why such a discrepancy? I guess this is more of a general question, but which models do I believe??
Thanks!
Mark