Antibody Structure Prediction

Question

[Alexander Skates]

I'm trying to predict the structure of a monoclonal antibody that does not have a crystal structure (and thus no PDB). I have the sequence for the heavy and light chain, and tried inputting it into Phyre2, but I wasn't sure how to treat the multiple chains. In the end, I just concatenated them both, which didn't seem to work as it told me the closest result was a glycoprotein.

How do I treat a protein such as an antibody, which is made up of multiple chains when predicting the structure?

Answer 1

[Sishuo Wang]

The following link might be helpful

http://zhanglab.ccmb.med.umich.edu/TACOS/

Also, SWISSMODEL might work if the Combine mode or Optimize mode is chosen I think. You may need to install SwissPDB-Viewer to do this.

http://swissmodel.expasy.org

http://swissmodel.expasy.org/SM_Oligomer.html