Hi
I need help with which two proteins interact, I would like to restrict some residues not process by the InterEvDock2. For instance, In my protein that is 1000 aa, Only I want to focus on the range of 200-500 residues. If an example to upload a list, please let me know.
Nail
Session information:
- id: 25eba3792d50d177a67f5703cbb375e6
- email: beslinail@gmail.com
- activated?: False
- authenticated?: True
Job information:
Hello,
apologies for the long delay in replying.
Your job had failed due to some issues on the server, they have now been corrected.
I re-ran your job successfully (using the PDB structures as input) : https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#jobs::InterEvDock2.G03965807651043
However it took a long time because of the large size of your proteins (and twisted shape of protein A).
Regarding your question, currently there is no way to “mask” a region of one protein when docking. Although we think it would be an interesting option, it is not easy technically and therefore will likely not be implemented in the near future.
In your case, my advice would be to restart a docking job using as PDB input only the region of interest from protein A (residues 200-500). The job will likely be much faster and the surface of the protein should be sampled better, because sampling will not be hindered by the other regions.
Please let us know if you need any more information.