[Chimera-users] Building protein-protein complex with known interacting residues

[fei.wu at chem.utah.edu]

Dear Chimera Team,

I am studying the interactions between three enzymes with their biological
assembly structures available in PDB. Using mass spectrometry, I have been
able to identify interfacial residues, and what I want to do is build up a
super complex (made of the three proteins) in a desired way that these
proteins are oriented by interactions between experimentally-determined
residues. Would you please tell me that, if I can make or draw this in
chimera? And I am also trying to compare experimentally-proposed complex
structure with simulated structure. Is there a specific way in chimera to
simulate interactions between two or more proteins? I found that when I
opened multiple protein files in one session, chimera would gave me a
complex of these proteins (not always true with different pdb files). Is
this an automatic generation of simulated protein complexes or just a
superimposition of part of proteins?

Thanks,
Fei


-- 
Fei Wu, Ph.D. candidate
Shelley D. Minteer Group
Chemistry Department
University of Utah
Phone: 385-234-0603
Email: fei.wu at chem.utah.edu