Fall Science Chat!

Science Chat November 1 in veteran chat

I’m thrilled to announce that the Fall Science Chat will be next week on Wednesday, November 1st at 10:00pm GMT (3:00pm, 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. 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: Wednesday, November 1st, 2017
Time: 10:00-11:00pm GMT; 3:00-4:00pm Pacific Time Zone
Location: #veteran chat

http://www.thetimezoneconverter.com/

(Thu, 10/26/2017 - 19:15  |  15 comments)
Joined: 09/24/2012
Groups: Go Science
Is an entry point needed for ligand?

You mentioned a paper with crocodile jaws allowing the entry of a drug or ligand. I wonder if an entry point is obligatory, or is it possible that a protein forms and surrounds completely a ligand ? Then with no entry or escape point.

Joined: 09/24/2012
Groups: Go Science
Ligand/drug destruction by protein

In the aflatoxine exemple, I understand that a protein could destroy or deactivate a ligand by bonding to it.
Is it the case for drugs? (protein destroying the drug)?

LociOiling's picture
User offline. Last seen 3 hours 7 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
enzymes 101

I just noticed that a video "How Enzymes Work" is currently featured at rcsb.org:

https://pdb101.rcsb.org/learn/videos/how-enzymes-work

It shows an enzyme extracting an H- and an OH- from its target. Then the target flips around, and an H- and an OH- are inserted in different spots.

The video mentions that some amino acids in the enzyme help hold the target in place, while others act as an acids or bases, donating or removing hydrogens.

Foldit doesn't have a way to model this kind of dynamic behavior.

In Puzzle 1440, the goal was to break up a lactone group in the aflatoxin. Making more hydrogen bonds with the protein may or may not help.

Can the scientists take us through the expected changes to the aflatoxin? Presumably, there's a way to do it in the chem lab without an enzyme, so it might be helpful to see how that works.

(Of course, we'll be on to the next phase of the aflatoxin challenge by the time of the chat.)

Joined: 09/24/2012
Groups: Go Science
Interesting videos

They seem to answer to my questions

Joined: 05/19/2017
Groups: None
Playerbase Demographics

When was the last count taken for this sort of thing? From what I know the playerbase right now tends to be older and I don't see too many of my peers folding yet. Some updated numbers could be useful for scoping out the state of the game.

Joined: 09/24/2012
Groups: Go Science
Which candidate design to evolve ?

It sounds that the first steps of a gaining solution are the most relevant for Science. This happens after 3-4 days "playing".

Then the latest days are "only" useful to check the full (score) potential of the candidate solution.

At the end, trying to get the 2 latest points in order to gain the race, we might think we "loose our precious resources" (from a science point of view - I don't consider fun !).

The problem is that, at day 4, we don't know in advance which candidate solution will be the right one. We can share to Scientists and continue to evolve the current "most promising one" - most of the time, at day 4, we simply continue with the best scoring one.

I understand that the Sketchbook goal is to encourage us to work more manually, and trying more candidate designs. It sounds like you would be able to identify a good candidate design on day 4.

Is there a way to help the players (incl. evolvers) to select the best "science" candidate after several days of semi-manual design?

Joined: 03/08/2012
Groups: None
Learning from other players & Chat time & date stamp

For improving my own folding skills I would like to see - from each 'expired' puzzle - the best ranking solution loadable into my solution e.g. as a reference/guide - full colored.

Fold.it-app chat should also print date & time (after an ongoing chat paused for a certain time). My laptop might run the whole day, but I'm not sitting the whole day in front of the screen.

Joined: 06/06/2013
Groups: Gargleblasters
a "good" ligand bond

when bonding to a ligand, is it better that there be no bindable but unbound sidechains? For example, if a GLN fits and binds just right with only one arm, is that a bad bond compared to another AA that has only one bindable sidechain?
sorry to bore you better chemists....

Susume's picture
User offline. Last seen 24 min 15 sec ago. Offline
Joined: 10/02/2011
Foldit Design update

Could you give us a quick update on foldit designs? How many have passed the Rosetta test, how many have passed the wet lab tests, how many have been crystallized (even if not yet solved)? Are the successful ones all the same shape? (I heard a little about this after the aflatoxin launch, but I know others want to know too).

alcor29's picture
User offline. Last seen 18 hours 33 min ago. Offline
Joined: 11/16/2012
Foldit scoring functions

Is there anything to report on a possible current effort or progress being made in rebalancing or refining the accuracy of foldit scoring internally as opposed to externally by using filters?

Joined: 09/24/2012
Groups: Go Science
Helix bias

I've read that the Foldit optimizer has some bias in favour of helices. Is this bias random? If not, why can't you correct it with some filter penalty?

Joined: 09/24/2012
Groups: Go Science
Membrane proteins

For membrane proteins, orange should be outside. Do you correct the scoring function for these "lipidic" (or partially lipidic) puzzles?

Joined: 09/24/2012
Groups: Go Science
The secret of drug design/production

Now we can design drugs. Once you have a drug design, how can you produce this exact drug in the labo?

alcor29's picture
User offline. Last seen 18 hours 33 min ago. Offline
Joined: 11/16/2012
Aflatoxin 1445

Aflatoxin 1445

The reverse (grayed/frozen) side of the aflatoxin grabber seems to have the structure of an ideal funnel trap to let the aflatoxin enter or even be 'sucked' in. If that's true and the funnel side-chains don't clog the passage, what we need to do is to block the rear entrance and 'grab' the aflatoxin in the 'pocket' like a baseball in a glove to keep if from getting through or backing out. What do you think?

smortier's picture
User offline. Last seen 1 day 19 hours ago. Offline
Joined: 03/10/2016
Groups: None
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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, Microsoft, Adobe, RosettaCommons