Winter 2018 Science Chat!

Science Chat March 8th in veteran chat

We're excited to announce that the Winter Science Chat will be next taking place on March 8th at 8:00pm GMT (12:00pm, Pacific Time Zone). If you have questions for our developers/scientists it would be helpful to post them right here so the team can review them in advance. We will be having Justin Siegel joining us, so feel free to ask questions about aflatoxin. If we aren’t able to answer all your questions in the given time, we will attempt to get a blog post up soon with answers. Despite the fact that this chat will take place in #veteran, it will be accessible to all who want to join via the following link: http://chat.mibbit.com/?channel=%23veteran&server=irc.fold.it. Looking forward to chatting with you all!

Date: Thursday, March 8th, 2018
Time: 8-9pm GMT; 12-1:00pm Pacific Time Zone
Location: #veteran chat

http://www.thetimezoneconverter.com/

For anyone that missed it, here is the log!
http://fold.it/portal/node/2004878

(Sat, 02/24/2018 - 00:03  |  19 comments)
Susume's picture
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Monomer design update

How many of the ~75 foldit monomers you ordered genes for last summer ended up passing the wet lab tests? Did the successful ones have a variety of different shapes? Have you ordered genes for more foldit monomers? Has our rate of passing the Rosetta tests gone up further since last spring's blog posts?

S0ckrates's picture
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Any plans to refine the ranked leaderboards?

As it stands, with the leaderboards being more or less static, I'm finding it a bit boring to grind. Any ideas to 'sweeten the deal' or 'shake things up'?

jeff101's picture
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Groups: Go Science
Evolver Hall of Fame?

We already have a Soloist Hall of Fame at
http://fold.it/portal/players/s_ever
Why not have an Evolver Hall of Fame as well?

S0ckrates's picture
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Besides that

That leaderboard is even more unmoving and static. I'm not talking about that at all!
Where I'm coming from: A lot of different competitive games have "seasons" where the ladder gets reset every season and people fight to the top cyclically. It's a more accurate reflection of a dynamic, churning game and the change in competitive strategies and players that come with it. With every season "bookended" as it were, developers and players can see what they want to change during and in between a season.

S0ckrates's picture
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Season Rewards

Another boon of the seasonal system is that it allows developers to incorporate ranked rewards for leaderboard/ladder positions in the greater season. What those rewards are depends on the game, however.

Joined: 05/19/2009
Groups: Contenders
https://alz.org/

S0c, Maybe this will give you some impetus to keep going ?
https://alz.org/
http://www.alsa.org/

S0ckrates's picture
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Yes, but...

Supporting a great cause is, indeed, well, great. I won't argue with that!
But my focus is more on the game aspect. How can Foldit as a game stand on its own two feet and keep people playing in absence of the citizen science aspect? I do acknowledge that a game is the sum of its parts and nothing is ever in isolation, but I find it to be one of the weakest aspects of Foldit right now, and a major roadblock for me to promote playing it to my friends.

Edit: As I was publishing this a relevant quote came to mind that sums up my stance. Here's a 6 second clip of the current President and COO of Nintendo of America, Reggie Fils-Aime: https://www.youtube.com/watch?v=3MlNWYyVdh0
The 1 minute monologue that this clip is from was from E3 2017, talking about the Nintendo Switch.

jeff101's picture
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Aflatoxin Puzzles

I'm curious if any of our designs looked interesting
and if any have been synthesized or even crystallized.
What features did the most interesting designs possess?
If there will be another round of aflatoxin puzzles,
how would you change the way our designs are scored
to better reflect which ones you found most interesting?
Finally, which aflatoxin orientation gave the best results?

jeff101's picture
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Aflatoxin Puzzles

If any of our designs have been synthesized,
do they seem to fold properly? Do they bind
aflatoxin better than previous designs? Do
they bind aflatoxin as well as you wanted?
Do any degrade aflatoxin?

frood66's picture
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science chat

can we get back to basics please? the client is unreliable.

newbs have issues even accessing.

Look at the numbers - they speak for themselves.

Keep this up FC....what do u think u will end up with?

I'm not being 'funny' - just looking at the elephant in the room.

But golly - u have always ignored B4....look what u have now...congrats on that.

Joined: 09/24/2012
Groups: Go Science
chirality

How is the numbering of the residues determined?

Would we find the same solution if the numbering was reversed ?

LociOiling's picture
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I'll take the first part...

Amino acids are combined into proteins by ribosomes.

The ribosome chains each amino acid to the next by a peptide bond. The first amino acid in the chain (now called a "residue") becomes segment 1 in Foldit. It's the first to leave the ribosome, but the rest of the chain soon follows.

Fun fact, methionine is always the first residue, see start codon. The starting methionine is often removed in post-translational modification.

For the second part, take a look at "protein palidrome" or "peptide palindrome". Partial protein palindromes are popular, and even pervasive in the PDB.

Check out A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins from 2008, which states:

One might expect that reversing the sequence would result in folds that are mirror-images of the original fold. However, there exists theoretical and experimental evidences that sequence reversing results in the same rather than the mirror folding, presumably due to the fact that both native and reverse proteins have the same amino acid compositions and/or similar hydrophobic-hydrophilic patterns. Evidence suggesting reverse peptide sequences result in different structures has also been presented in the literature.

So perhaps a perfect protein palindrome is possible...or perhaps not.

Joined: 09/24/2012
Groups: Go Science
default size of the hydrophobicity for successive sheets

When starting de novo, I try to make the hydrophobicity on the same size for successive sheets.

However, the starting flat protein often reverse the hydrophobicity between successive sheets.

Is there a reason for this default alignment?

Joined: 09/24/2012
Groups: Go Science
ok thanks Chat

The answer in the chat is what I wanted: this starting rotation has no meaning and I may rotate successive sheets like I want.

S0ckrates's picture
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Membrane Hydrophobicity Simulations

Is it possible to simulate a hydrophobic region in Foldit for the sake of puzzles involving proteins with external hydrophobic domains for cell membranes? I've always wondered about designing little cellular molecular spaceports for receptor molecules and having a little fun with that.

jeff101's picture
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Membrane Monomer Design Puzzles

Is it possible to have some of the Monomer Design Puzzles be for membrane proteins, with hydrophobics on the protein exterior and hydrophilics in the protein core? That would put a new twist on a common puzzle type. Would the Building Blocks in the Blueprint tool be the same for membrane proteins? Would remix & rebuild need to be changed to treat membrane proteins?

Joined: 05/19/2009
Groups: Contenders
Formal Education

My Foldit experience has raised my interest in becoming formally educated in bioinformatics. Is there a way for non-US citizens to attend online courses with certification in this field by either University of Washington or UCDavis ?

I may not be able to attend the online chat, but an answer to the question would be much appreciated for later offline reading.

bkoep's picture
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Good question!

There are a lot of options for continuing education, and the best choice will depend on your specific motivation/intention. UW does offer a handful of online programs that accept international applications, and you can read about them here:
https://www.pce.uw.edu/online

It's worth noting that many online programs do not offer accredited degrees, but only award a "certificate" upon program completion. These certificates are no substitute for a university degree, which is a strict requirement of many job applications. My understanding is that these certificates are most often used to boost the résumés of university graduates who are otherwise qualified, but are simply looking for a leg up when applying for jobs in very specific fields (e.g. a graduate with a bachelor's degree in biology might pursue extra certification before applying for competitive jobs in the pharmaceutical industry).

If you have in mind something in particular, feel free to send me a PM and maybe I can offer more pointed advice!

Joined: 05/02/2018
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Thank you

Thank you

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