[Chimera-users] Question regarding protein-protein interactions in ChimeraX

[Dr. Kevin M Jude]

Hi Camille,
The coordinate files from the PDB are independent of each other and each has its own reference frame; unless a single structure contains a complex of the two proteins, any overlap or contact between them is just a coincidence. You can use existing mutational, biophysical, genomic data, etc., to begin to make a testable prediction of the interaction, but ChimeraX is not aware of any of this.

Best wishes
Kevin

From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Lake, Camille (NIH/NIAID) [C] via Chimera-users <chimera-users at cgl.ucsf.edu>
Date: Sunday, October 30, 2022 at 4:42 PM
To: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Question regarding protein-protein interactions in ChimeraX
Hello,

My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space.

Thank you,

Camille

Camille Lake, PhD
Emerging Leaders in Data Science (ORISE) Fellow
National Institute of Allergy and Infectious Diseases (NIAID) - Office of Data Science and Emerging Technologies (ODSET)
National Institutes of Health (NIH)
5601 Fishers Lane, 6C5
Rockville, MD 20871
camille.lake at nih.gov
301-761-7976
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