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/
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.
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)?
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.)
They seem to answer to my questions
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.
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?
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.
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….
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).
