Scientist Chat 4/4 1:00pm PDT

On the heels of our last devchat comes a highly requested scientist chat! Come chat with our scientists in #global on Thursday 4/4 from 1:00-2:00pm PDT / 20h00-21h00 GMT. We’re on Pacific Daylight Time here in Seattle (-7 GMT) so don't forget to double check your time zone conversion. A transcript will be available on the site after the chat for those who can't make it.

If you need help getting into #global chat, check out this helpful guide for assistance.

Thanks and we’ll see you there!

Edit: A transcript of the chat is now up for those of you who missed it.

- katfish

*Thank you to everyone for correcting my GMT conversion. Sorry for the epic derp!

( Posted by  katfish 79 2078  |  Wed, 03/27/2013 - 17:08  |  5 comments )
brow42's picture
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Some questions for the scientists

I may not make the chat, so here are 4 questions that I can remember (I'm sure there's lots more I've been saving up but this will do for today)

1) I was really unhappy with one of the CASP puzzles because it folded around zinc atoms. Here's my feedback. . The frustration in that feedback isn't really directed at Foldit, but at CASP. How can we, or even the computers, correctly predict the structure if it's missing key parts? What was CASP thinking? What can we do about this?

2) About a year ago you said you were getting new equipment that would allow you to synthesize far more of our designs than before. But your recent blog post suggests you're still doing it by hand in a very low-throughput way. What's the status of that upgrade?

My other questions are more technical. I know you want us to use our creativity to make unusual designs, but I don't like trying to fold against natural trends that I can't even perceive. Maybe someday we'll have 3-D Foldit with haptic feedback gloves! But until then, I'd like some guidance.

3) Sidechains in a sheet normally alternate, but sometimes they don't. They form beta bulges in sheets, and they are particularly common in server predictions, perhaps from aggressive hiding of hydrophobes. But there are two ways of doing this: twisting around omega, and twisting psi/phi. Which is the 'correct' way of doing it, that would fold naturally? Also, one player ended up with one of these in a sheet that could not be untwisted with tweak, only with rebuild.

4)The Koga-Koga paper was very interesting. I know you don't want us to just copy those designs, but you DO want us to make stable, self folding designs. Could the information in that paper be presented as a simple set of rules with simple visualization? I'd hate to be making a design that won't fold properly because I was fighting some inherent bias in the protein. A lot of my choices (left-right, top-bottom) are just coin flips.

gramps's picture
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Joined: 12/16/2010
stated times not consistent

PDT Time details:

"Time zone offset: UTC - 7 hours", but

21 minus 7 is 14, so 21:00 UTC is actually 2PM PDT.

If 1PM PDT is intended, that's actually 20:00 UTC.

gramps's picture
User offline. Last seen 3 years 21 weeks ago. Offline
Joined: 12/16/2010
Time Zone Conversion

For additional confusion, you can try this set of time zone conversion tools on the wiki ;-)

Joined: 02/08/2012
Exposed Residue Rurials

Buried hydrophilics are shown as blue, but there is a lot of other colors that appear; a lot of magenta's, purple's, pinks, and probably many more. What are these other colors indicating?

Joined: 08/10/2010
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your questions

Hi everyone (especially brow42); sorry I couldn't answer all these in Foldit chat; lots to talk about and we had limited time. Let me know if you need more information; this is sort-of the quick version: (for 2,3,4; I'm not involved in CASP.)

2. we might not have quite the high-throughput system we were expecting; there were some issues. (I don't know all the details.) However, we are planning on ordering some recent designs super-soon, if we haven't already. Specifically, some of the helix bundles (and other stuff from that puzzle) that David Baker mentioned in the scientist chat today. I know that puzzle 691 (tetramer design puzzle) was giving players a lot of problems, but it's also the puzzle that has produced some of the most viable-looking, exciting designs so far. (Even the normal, boring-looking super-long helix bundles are pretty good; those are among the designs we'll be ordering.) We'll let players know when we've looked at some of these designs, even if they don't work as-designed. They're long enough that they'll have to be made as proteins, not as peptides.

3. beta bulges are actually kinda bad, energy-wise, vs. straight sheets. (But admittedly, nature does use them a lot. Probably to get to a specific shape that it wants a protein to be, and also to prevent strand-edge aggregation, since the regular and exposed pattern of backbone amides at the edges of beta sheet is a recipe for aggregation if there isn't charge repulsion or sheet distortion to fix it.) And definitely don't twist omega, assuming you're talking about the amide bond angle, which should always be flat (as close to 180 as possible; even a few degrees off is very bad.) Phi/psi is always the way to go. I've noticed some examples of "untweakable" beta sheets myself; often it depends on what they're attached to. Rebuild or manually tweaking them can work. Sometimes I resort to all-atom mode (under view) and make specific, tight constraints between atoms to manually force the H-bonding pattern I'm looking for. More time-consuming, but it works.

4. The Koga-Koga paper is great, yes - though we aren't advertising it (or other design stuff) super-heavily because we're okay with players breaking the rules once in a while (like nature does.) Especially since they're just guidelines, really. But you have the right idea - we do want to get this information out there more than we have; if more players follow the design rules in this and other related papers, the designs will probably be more viable overall. :) A co-worker of mine will provide you with a better answer later, because he's been giving this particular issue (getting better design information out to the players) more thought.

@drumpeter: I always set color: score/hydro + CPK when I play, which sets the atom colors by element and helps me identify the residues (and H-bonding opportunities) more easily. But... sorry I don't have a good answer for your actual question; I'm actually not up on the recent color-coding for the buried vs. exposed hydrophobics/hydrophilics. (I know some of it has changed recently and is different in my old local build.)

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