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

Aldo Segura aldosegura at gmail.com
Mon Mar 3 10:40:53 PST 2014

Dear Fei,

I think you might do that in Chimera, but it will be merely illustrative
because you don't know the correct orientation of the proteins into the
complex. I think you should go first for protein-protein docking program to
predict the orientations of the proteins into the complex. Moreover, you
can filter the docking predictions by keeping those that are according to
your experimental results and then, visualize the predicted complexes in
Chimera. For example, you can try with ClusPro server:



2014-03-02 15:08 GMT-05:00 <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
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Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera at cchmc.org <asegurac at ipn.mx>;
aldosegura at gmail.com
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