UCSF ChimeraX pushes drug discovery into virtual reality

Virtual reality has been out there for the gaming industry for more than ten years and it’s a very strong.

Virtual reality has been out there for
the gaming industry for more than ten years and it’s a very strong field. But
actually using this technique to actually understand proteins and how
this understanding can lead to new drugs, this is a relatively recent field.
And the UCSF ChimeraX team, they are pioneering this field. All of our
research really revolves around trying to understand how protein structures and
other biological three-dimensional structures what they tell us about how
the proteins work, and then ultimately exploiting that for drug discovery, how
can we develop drugs that will target these proteins. I try to understand from
a computational perspective how proteins work and how can small molecules bind to
this protein and affect its function, potentially providing new hypotheses for
new therapies VR has completely changed things now with the ability to walk into
a scene and be able to see things from multiple directions. Using it a couple times, especially here
in discussions and lab meetings, I found that it was extremely useful and
everyone can step up, put on the headset, and point at something and we can
discuss ideas on the go. We’ve used Chimera for years. It’s one of
the best software out there for visualizing proteins and other
biological structures. And of course Tom Ferrin, who develops Chimera and ChimeraX,
is a colleague in my department. UCSF has been a leader in this area for decades
now and there’s very few academic research labs developing software at
this caliber. It provides much more of an intuitive feel for proteins for
especially for people who are not experts in them. Beth, at some level, you
know, she’s an incredible expert in this field of protein kinases and the role in
cancer. But being able to sit there with her and look at the proteins in 3D, all
of a sudden, you know, she could get very very quickly an intuitive feel for how
the protein structure is related to its function. Pediatric patients with
high-risk leukemias may give a sample of their leukemia cells to be molecularly
profiled. We have these new targeted medicines
that work against specific mutations that cause cancer, but the proteins can
change in a way that they can no longer be blocked by the medications. The VR room was great. That’s where our
meetings were held and so we all knew that we were on the same page. If
somebody was talking about a certain loop in the protein you could actually
walk into the protein with them and they could point at it and actually show you,
so it’s not like you’re looking at a two-dimensional picture making sort of
guessing whether or not you’re talking about the same residue. In this scenario
we were able to just focus on just certain important mutants rather than
look at every possible mutant out there. Qualitatively, I can say, being able to
walk into a protein, look at it from multiple perspectives, I mean literally,
you know, putting my head in the middle of it, it leads to insights that I think
I just wouldn’t have had otherwise

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