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Joined: 09/21/2011
Groups: Gargleblasters

Has anyone seen the alerts on Chikungunya Virus?

CDC issued a warning. No vaccine, no treatment. Patients are wracked with pain for days on end.
I don't know how to go about this, but would there be some way to contact researchers to get Chikungunya in our queue? This seems like a good one to get sequenced.

Joined: 04/15/2012
Groups: Beta Folders
Yes, definitely. I'd contact

Yes, definitely. I'd contact KatFish our BK. Not sure if BetaHelix is available.

katfish's picture
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Joined: 01/09/2013
Great idea

Really interesting article, andrewxc. Definitely something we can look into.

v_mulligan's picture
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Joined: 03/04/2009
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Good target

A number of the proteins in this virus have structures that have been solved by x-ray crystallography (including the envelope glycoprotein responsible for getting the virus into host cells). There are also low-resolution cryo-EM models of the whole virus. That's not to say that there's nothing left for Foldit players, mind you. On the contrary, given the structural information available, this could be a good target for which we could try to design a protein binder to block viral infectivity.

We'll keep this one in mind for a future puzzle. Thank you for suggesting it!

Joined: 09/21/2011
Groups: Gargleblasters
Nature Article


Sorry for the Res. Found a crystallography scan in Nature. Not sure if you guys would want it, or if a player could make a side-contest for a binder...
See inset figures.

Joined: 09/21/2011
Groups: Gargleblasters
Now what?

It seems like a binder would be what professionals would be trying. I got a ton of information from a friend. Now what do I do? How do I create a puzzle? I was linked to Rosetta from the "how do I create my own puzzle?" topic; I'm just curious where to go from here (my guess is that I shouldn't start stalking the author of the articles until I know what I want from him...).

Protein templates: http://www.proteinmodelportal.org/?pid=modelDetail&provider=MODBASE&template=3trkA&pmpuid=1000138234226&range_from=1&range_to=&ref_ac=3GPG&mapped_ac=Q8JUX6&zid=async

Previous Nature link has structures.

Joined: 04/15/2012
Groups: Beta Folders
Well, there's the academic

Well, there's the academic standalone: tinyurl.com/academic-foldit

It's a Rosetta addon. From that, if you want an actual puzzle, whoever's doing the research would have to contact the devs to get one up, far as I know.

Joined: 09/21/2011
Groups: Gargleblasters

I have that, but it's unpacked in my FoldIt folder and I don't know what to do with it... Or do I need to download Rosetta? Sorry, I'm unfamiliar with anything other than FoldIt... :(

Joined: 04/15/2012
Groups: Beta Folders
It sounds like it's a Rosetta

It sounds like it's a Rosetta extension, so yes, you would have to license Rosetta (to my limited knowledge).

Joined: 04/15/2012
Groups: Beta Folders
I might EMail Seth via the

I might EMail Seth via the address on that page, as he's lisetd for technical help.

Joined: 04/20/2012
Groups: Go Science
Rosetta@Home is running Chikungunya calculations

I have 2 laptops running jobs for Rosetta@Home.
Both of them are doing Chikungunya calculations
right now.


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons