Developer Chat

@katfish Hi everybody! We'll be starting the Scientist Chat in just a few minutes! 12:54
ComputerMageIRC Hi Kat! 12:54
auntdeen2 hey folks - scientist chat in a few - please use puzzle chat for all non-scientist questions & comments and be patient 12:54
auntdeen2 hi kat :-) 12:54
@katfish Hey there, CM! 12:54
@katfish and auntdeen ;) 12:54
auntdeen2 kat - brow can't be here but posted questions in scichat thread 12:55
auntdeen2 can you make sure the devs see them? 12:55
brow42 I made it, but very sleepy. 12:55
auntdeen2 ah - thought you had to leave 12:56
ComputerMageIRC I will be on a chat only for 20 minutes and thwn I have to run for a meeting. But I have some questions 12:58
@katfish Yep, saw brow's questions in the thread 12:59
@katfish brow, I will make sure they address those! 12:59
@betahelix Hi everyone, we'll start the Scientist Chat with DrLemming and I in a couple minutes! 12:59
bcaa_irc drlemming? :D 13:00
eromana hello everyone 13:00
bcaa_irc is this his real name? 13:00
auntdeen2 yes bcaa 13:01
auntdeen2 hi beta and drlemming :-) 13:01
bcaa_irc oh interesting, probably of german or jewish decent... 13:01
@betahelix So the plan for today's Scientist chat is: 13:01
TheGUmmer hi beta, hi DrL 13:02
@DrLemming hey. :) 13:02
@betahelix I'll start by talking about CASP10, then DrL will talk about design, and then at the end of the chat David Baker will stop by for a little bit :-) 13:02
@betahelix Hi everyone! 13:03
ComputerMageIRC Hi DrL, Beta! 13:03
@betahelix And we will make sure to address the questions in the comments: 13:03
@betahelix 13:04
@betahelix Now, let's get started with a CASP10 recap! 13:04
@betahelix So, the CASP10 results have been up for a while on the CASP webpage (most of the natives have been solved and released) 13:05
@betahelix If you looked at the results you saw that Foldit did quite well in the Refinement category! :-) 13:06
@betahelix (and I'll show some results on that in a little bit) 13:06
ComputerMageIRC Can you give a direct link to that page? 13:06
marie_s the link is in german wiki 13:07
Aotearoa Hi Betahelix. 13:06
@betahelix 13:06
@betahelix The Template-Free category is always a very tough one, and unlike in CASP9, there was no amazing de-novo prediction in CASP10 13:08
@betahelix In CASP9 there was one amazing prediction that was highlighted by the assessors. It had been generated by the RosettaServer and the best prediction came from the Void Crushers (the was in the NSMB paper) 13:09
@betahelix But this year, that was a very tough category... and no group really "nailed" any template-free target 13:09
@betahelix The Template-Based category was different, where lots of CASP10 teams were able to do well (these are the targets where there is already a close structure that you can start from, or many templates) 13:11
AsDawnBreaks Would template free mean free design denovo? 13:11
Aotearoa woohoo great news. 13:11
@betahelix yes 13:11
@betahelix but this one was a lot harder for Foldit, because unlike the other CASP10 teams (who get to use many bioinformatic tools) all we gave you was an extended chain and the Alignment Tool 13:11
@betahelix Even with just that, though, many Foldit players were able to do very well.. the main issue is that we have trouble selecting these models. 13:12
@betahelix This leads me to my first table that I want to show you: 13:12
@betahelix 13:13
@betahelix (can everyone see that?) 13:13
marie_s yes 13:13
utaca yes 13:13
@DrLemming looks good. 13:13
CFC it does :) 13:14
@betahelix So, what this table shows you is the best Foldit prediction in the set of models that was filtered by the WeFold team... 13:14
@betahelix so clearly you generated some amazing predictions (most of them are a lot better than the starting refinement model) 13:15
ComputerMageIRC What meant "Any Group"? 13:15
Madde what's the last column? every solution of Foldit players or only the ones FoldCentral and the three teams submitted? 13:15
@betahelix and had we been able to pick them out, they would have beat the predictions selected by the other participants at CASP10 13:15
Aotearoa how did you do that? 13:16
Susume2 last column is the other casp competitors 13:16
utaca a they were not submitted? 13:16
@betahelix the last column is the model that the CASP organizers deemed to be the top-prediction 13:16
Madde ah, ok 13:16
@betahelix So, in terms of the refinement category, the last category highlights the winners of each of those targets 13:17
@betahelix But clearly you generated better models than what they picked out!!!! 13:17
@betahelix Unfortunately, we are very bad at selecting those :-( 13:17
ComputerMageIRC That means that we did good in 65% of the cases? 13:17
@betahelix What is interesting is that you also seemed to get better as CASP went on ;-) 13:18
ComputerMageIRC I really love CASP puzzles! 13:18
@betahelix but that could also be because the first refinement targets were smack in the middle of CASP10, whereas eventually those were the only ones to work on 13:18
ComputerMageIRC Way more than design one (where you don;t know what you are expected to make ;) 13:18
@betahelix So, we've known for a while that we are very bad at selection, which is why 3 Foldit Groups asked us before CASP10 to be able to pick out THEIR OWN group's submissions 13:18
AsDawnBreaks @CMI actually prefer the non-templated denovos. I can do a lot more with them. 13:18
ComputerMageIRC gotta go for meeting. Will read log later. But I would like to talk about electrostatics in folding. Looks like it works (I used it in manual folding) as I was quite close to native in 686 13:20
@betahelix ok.. bye CM! 13:20
@betahelix The next figure I'm going to show you shows you which group submitted the best prediction for each CASP10 refinement target 13:20
@katfish Have a great day, CM! :) 13:20
@betahelix BUT, it's sorted by the Improvement in GDT over the starting model 13:20
@betahelix 13:21
Madde link to the presentation about refinement targets (PDF): 13:21
Madde 13:21
grampsIRC woohoo! AD got one :-) 13:21
@betahelix so basically, how much did the very best prediction submitted to CASP10 (by any team) actually improve over the starting refinement model that the organizers gave us 13:21
Aotearoa hi katfish 13:21
@betahelix So, obviously the FEIG group "won" the refinement category in CASP10, but you can see that a lot of their "winning predictions" didn't actually improve over the starting model much 13:23
@betahelix for anyone interested: Michael FEIG, utilized many independent explicit solvent molecular dynamics simulations, which you don't have access to, since Rosetta currently doesn’t include explicit water molecules… 13:24
@betahelix so someone should add that to the feedback ;-) 13:24
@DrLemming Rosetta with explicit water molecules? That wouldn't run slow at ALL. :P 13:25
Aotearoa entrophy? 13:25
brow42 FIEG may have had small improvements, but ours, then, were even less 13:25
@betahelix But, if you look at which targets had the best improvements, Foldit is at the top! 13:25
alwen When we are good we are very very good 13:25
@DrLemming So basically, we're beating nature at its own game... except that the point was to mimic nature? Still, Foldit players are awesome. :) 13:26
@betahelix And AD, Void Crushers, and one of the WeFold branches were all able to find those! 13:26
brow42 It looks like Foldit players make big changes, even if only small changes are required. But the other teams miss the big changes when required. 13:26
@betahelix Exactly... 13:27
@betahelix When Foldit wins, it wins big, but when we select poorly (because we were brave) then it really hurts 13:27
AsDawnBreaks Our interface and community have some big advanteges in that respect. 13:27
@betahelix I think the take-away message is that selection is still the main issue... but that you are much better at it than we are! 13:28
marie_s did you know if other teams select better? 13:28
@betahelix @marie I know that the Baker Lab doesn't! 13:28
Aotearoa i believe some of us can see that a certian shape and or design will perform better, more stable by what aminos are in what kind of order... if that makes sense. 13:28
@betahelix But I'm sure that other CASP groups will argue that they too have this problem, and they generated better models as well (that they didn't select) 13:29
@betahelix Which leads me to Hand-Folding... 13:29
AsDawnBreaks Could groups over x amount of global points be able to have a tool to submit their own? 13:29
@betahelix I want to show you a couple plots. First is the RMSD plot of Puzzle 683 13:30
brow42 You have almost 18 months to make that tool :) 13:30
@betahelix 13:30
Susume2 AsDawn, the groups who requested to submit their own, were able to 13:30
AsDawnBreaks I'm just suggesting make it more available, and suggested. 13:31
auntdeen2 Dawn - it is a lot of work 13:31
@betahelix you can see that if we selected the best Foldit score (lowest Rosetta energy) that would not be the solution that is closest to the native (you want to be as far to the left as possible) 13:31
@betahelix whereas if you compare this to a very similar target, Puzzle 689b that was only hand-folding: 13:32
@betahelix uh oh... lost that plot! katfish, emailing you that right now! (sorry gang!) 13:32
* Madde facepalm 13:33
@katfish On it! 2 shakes everybody 13:33
brow42 Similar, how? Nobody recognizes these names except maybe Marie and Madde :0 13:33
@betahelix my bad, katfish will post it in a second... now we can build up suspense! 13:33
auntdeen2 beta - we have new players - quick explanation of graph? 13:33
alcor29 Tx auntdeen 13:34
auntdeen2 ;-) alcor 13:34
@betahelix So this graph show the energy landscape for the CASP T0709 Disulfide Repost puzzle 13:34
* CFC :) 13:34
@betahelix It was a freestyle puzzle, with templates, and had 3 disulfide bridges (which you all totally nailed :-) ) 13:34
@betahelix the rosetta energy (y-axis) is all that you see in the game as it corresponds to the Foldit score (except that just to confuse you, it's negative ;-)) 13:35
marie_s but we were not good at these puzzles in casp? 13:35
@betahelix whereas on the x-axis is the RMSD, representing how far from the native it is (RMSD = 0 is a perfect match, RMSD = 33 is awful) 13:36
@betahelix @marie the reason we reposted these puzzles after CASP is that it when you formed the disulfide bridges during CASP it doesn't score as high as if you didn't (so even those there were many predictions that were correct, they were not easy to pick since they were not the top-scoring) 13:37
@betahelix Now compare that RMSD plot to this one: 13:37
@betahelix 13:37
Madde BUT there was one big difference in those two puzzles: only the later one had 100 bonus points for each D-bond 13:37
@betahelix Puzzle 689b Hand-Folding CASP10 T0711 Repost 13:37
brow42 oh, that's right. and that explains the left hand edge of the plot 13:37
auntdeen2 wow - what difference 13:37
@betahelix @Madde, they both had the bonus... 689 didn't but 689b did :-) 13:38
Madde I meant T709 13:38
marie_s 13:38
@betahelix Obviously there are a lot less green dots ;-) but you'll also notice that the lowest Rosetta Energy, the top-scoring Foldit solution, the one that is very easy to pick out by score, is actually one of the closest 13:38
@betahelix @Madde, yes during CASP... exactly, that is why we added the Disulfide bonus, and these puzzles were making sure that solved the problem (which it did, right?) 13:38
@betahelix I need to wrap it up, otherwise we'll never get to talk about Design with DrL and David Baker... 13:40
Madde yes, but you were suggesting the hand-folding made the difference 13:40
brow42 The 709 plot shows two problems with the rosetta score....the bottom shows a broad distribution of high scoring solutions that are not correct, and the left edge show many correct solutions that could not reach the high score. 13:40
auntdeen2 does this indicate that our scripts work against us? 13:40
@betahelix @auntdeen that was what we might need to look into more... obviously there have only been 5 hand-folding puzzles so far: 13:41
AsDawnBreaks Depends on the goal, probably. Perhaps the scripts need more parameters from the puzzle. 13:41
@betahelix 13:41
marie_s in 686 the best score was not the best solution 13:42
firejuggler and if you coun't the -pre script era ? :p 13:42
@betahelix :-P 13:42
auntdeen2 beta - that page is broken 13:42
firejuggler yep, broken 13:42
marie_s we have no autorization 13:42
Aotearoa i'll hack it if you need some. 13:43
@betahelix katfish, can you poke jflat06 about that? 13:43
@katfish Yep doing that now 13:43
steveB So the scripts are finding an incorrect energy mimimum are tunneling down ? 13:43
@betahelix that was a link to the new Hand-folding category.. sorry gang :-( 13:43
@betahelix double epic fail for beta_helix today :-( 13:43
auntdeen2 some of us have seen our ranks but thought your page wasn't ready yet 13:44
auntdeen2 hey - it's still april fools week ;-) 13:44
@betahelix hahahaha :-P 13:44
@katfish Ok should be visible now 13:44
firejuggler i think the script, even if they contain randomness... aren't randow enough 13:44
@katfish Just had to publish it - derp! 13:44
@betahelix @steveB it might be that the scripts are able to find some Rosetta loopholes in the energy function! 13:44
@katfish Oh wait, spoke too soon. Gimme a minute. 13:44
AsDawnBreaks I've got it. 13:45
alcor29 Did both plots have the bonus? If not, how can you compare them? 13:45
firejuggler most script try to improve the worse area. But it might not be where there is the most point. 13:45
@betahelix @alcor29 yes, both plots have both bonuses 13:45
alcor29 tx 13:45
auntdeen2 fire - I suspect you are right 13:45
@betahelix Anyway, I just wanted to end on that... since those are very fresh results that I found very interesting when I compared the hand-folding vs non-hand-folding results... we'll look into this more! 13:46
@betahelix Let's move onto Foldit design... 13:46
@betahelix DrL, take it away!! 13:46
@DrLemming Whoo-hoo! Okay, first of all, apologies to everyone for how slow everything is; we're meeting every week to make sure that structures you design will behave well in real life, AND to do that with less filters! 13:47
@DrLemming ...we aren't there yet, of course, but there is progress. With some puzzles as notable exceptions, your designs from some recent puzzles are looking really great, and we plan to finally make &/or order some very soon. 13:47
@DrLemming (David Baker will mention more about that shortly, I believe.) 13:49
@DrLemming I have more I can discuss, but maybe it would be more useful to answer some design questions? 13:49
@katfish (MEEP: Hand-Folding page is visible now) 13:50
@katfish 13:50
@DrLemming We can tell you what we've been doing to get the best-scoring results to be (what we think will be) the best-folding, best-looking proteins, or we can answer general design questions. 13:50
marie_s since all is so slow , why did we begi de novo? 13:50
@betahelix thanks katfish :-) 13:51
Aotearoa can we please have a floating grid included into the white background where we could lay out sheets and helices onto this 3d grid, and pin on the backbone to the areas around the floating grid to design faster combinations of sequences 13:51
@DrLemming We start with an extended chain mostly so we don't bias you toward a specific structure. 13:51
@DrLemming It's actually not so hard to get from extended to a secondary structure of your choice quickly (just set chain to helix or sheet then select a segment and rebuild) ... it's the packing of secondary structure elements that's the tricky (and fun!) part. :) 13:51
Aotearoa yes agreed. 13:51
auntdeen2 DrL - we used to have what we called the "megahelix" problem back a number of months - that became weighted to not score so well - but on the puzzles with filters, the megahelix is alive and well again 13:53
AsDawnBreaks 've seen that. 13:53
@betahelix @Aot we'll have to save that question for the next Developer Chat, since I know there has been many feedbacks about having some sort of Pin tool to really freeze sections in 3D space (but that is tough to do with Rosetta) 13:53
steveB Agree with Auntdeen - it's a big problem 13:53
Aotearoa its hard to lay out sheets into a formal manner, to have a series of common shapes available to place on screen and drag over the protein to copy it (into the design) would be a faster way to identify a functional structure. 13:54
@DrLemming Hmm.. I haven't seen any megahelices in the top-scoring solutions recently, but I'll keep an eye out for them now that you've mentioned it. I sure hope those things don't get resurrected! To specify... 13:54
brow42 I think design needs to be less competitive, rather than trying to penalize stable but uninteresting shapes. 13:54
@betahelix do you mean beta-helices? sheets wrapping around like a helix, or am I the only one always thinking about beta-helices ;-) 13:54
@DrLemming do you mean pi helices or beta helices? That is, how "mega" are these helices? Helices that look just a little too big to be normal alpha helices are pi helices. Helices that are a LOT too big are beta helices. 13:55
auntdeen2 one big lonely helix 13:55
steveB One big long straight helix 13:55
Aotearoa <--- i used to make them all the time and they did score wel, but it may also give possible variation to common problems of binding to targets with helices rather than sheets(backbone and sequences) 13:55
auntdeen2 no matte the size of residues 13:55
@betahelix got it: one long helix (with symmetry they are parallel with one another) 13:55
@DrLemming OHHHH okay. That. The big lonely helices, gotcha. Okay, those are actually less evil, since they're actually semi-viable structures in nature, if a little boring. (Okay, a lot boring.) However: 13:55
@DrLemming if they pack against other helices in a bundle, that's not all bad. 13:56
@betahelix (David Baker will comment on how much he loves those ;-)) 13:56
auntdeen2 lol 13:56
auntdeen2 thanks 13:56
@DrLemming A lone helix in a monomer puzzle is not good. A lone helix in a trimer or dimer puzzle, that packs against copies of itself to form a 3-fold or 2-fold helix bundle, is actually a legit structure. 13:56
AsDawnBreaks Giant helix: That's my group. I wouldn't even evo if/when I start again. I can't do anything with it. 13:56
steveB So we are not wasting your and our time by building them then ? 13:56
alwen (but they are boirng) 13:57
@betahelix That'll be the first question we'll ask David :-) 13:57
@DrLemming ...though I agree, yeah, it's a bit boring - and larger hydrophobic cores should be able to score better if the chain length is long enough. (But with short enough chain lengths, e.g., ~25-30, helix bundle might be the legit best structures.) 13:57
Aotearoa i feel the variation is important to find new binding possiibilities 13:57
brow42 well, you only need to make a long helix once in your life and then you're done. 13:57
@betahelix need more beta helix... 13:57
@DrLemming Absolutely. And though simple helix bundles have been featured prominently in the top-scoring solutions as of late, there have been plenty of more creative stuff as well. 13:57
steveB Is this an appropriate time to ask about the Ubiquitin copy I made that scored low ? 13:58
@DrLemming Yes! 13:58
@betahelix I want us to address steveB's question from this design puzzle: 13:58
@betahelix 13:58
@DrLemming In fact, we're just linking to that: 13:59
@DrLemming ah, there we are. :) 13:59
@betahelix (perfect timing steveB, it's almost as if we planned that :-P) 13:59
Aotearoa My first question would be, can we start to design a new gui for protein designs? having some feedback so we can compete agasint some of the new software dbeing used by compeating teams from around the world. ie. concepts for protein design simplicity and to create a base to start from. inc templates from common natural sequences / shapes 13:59
steveB :) 13:59
@DrLemming So, all we can tell you at this point is that it's inspired us to look at a large range of native proteins; after you mentioned that, we're testing our design filters not only on Foldit player designs but also a set of native proteins. 13:59
@katfish Let's keep it on-topic everyone! Thanks :) 14:00
@DrLemming So though I don't think we can say that the issue is fully solved, we are addressing it seriously, and keeping a closer eye on native scores re. our filters. 14:00
markm457IRC DrL - to help us learn - would it be possible to post examples of our solutions which are "best folding" - all we currently see is "best scoring" 14:00
@betahelix @Aot sure... we'd need to bring that up in a Dev Chat, though... 14:00
Aotearoa ty. 14:01
steveB @markm4571 agree with that - it would help a lot 14:01
@DrLemming @markm457: Yes. Especially now that we're selecting some designs to finally synthesize. (To be honest, we've ordered a few before, but we haven't got any of them to work yet so I haven't mentioned it. :( ) 14:02
@betahelix @steveB native proteins aren't designed to be optimal-and nature is good enough to be able to break the rules when she wants to :-P 14:03
auntdeen2 oh - please mention it! we'd rather know that you are doing even if not working out yet! 14:03
@DrLemming But we can post examples of what would be more or less viable. In the long run this shouldn't be an issue, since our overarching goal is to get these filters good enough (and fast/efficient enough!) so that the top scoring stuff IS THE BEST STUFF! :D 14:03
@DrLemming But yeah, since we aren't there yet, we will give you some examples. I have some handy right now, but they're a bit specific to the hydrogenase puzzle we recently posted. Is that okay? 14:03
steveB I like rule breakers, does she want to join Void Crushers ? 14:03
@betahelix In your particular example, steveB, the solutions that scored WAY better than Ubiquitin had very different amino acid sequences than Ubiquitin, right? 14:04
CFC dibs Steve, I already PMed her :) 14:04
@DrLemming 14:04
auntdeen2 we have more mothers, sorry vc & CFC 14:04
Aotearoa careful steve posting stuff like that got me kicked from global once. 14:04
@DrLemming Ah, it works. Excellent. Okay everyone, look at the above fold: It scored REALLY well in the recent hydrogenase puzzle. Unfortunately, it also makes me sad. :( 14:04
Aotearoa AHAP are always looking. 14:04
steveB @betahelix Yes, thats correct 14:05
@DrLemming Mostly just because we wanted to incentivize a H-bond to the catalyst and some of the top-scoring structures didn't have one. (Our fault for not making the bonus big enough). But also: 14:05
alwen bedsheet fold 14:05
firejuggler design is too flat? you want more curves? 14:05
brow42 I really liked drumpeter's barrel around teh catalyst, I didn't think of might not fold but it looked nice. Will it fold? 14:05
@DrLemming It's almost entirely covered by hydrophobic residues, and the beta sheets would likely aggregate via edge-to-face interactions. 14:06
@betahelix @steveB hopefully Ubiquitin has the best fold for that exact sequence... but when you can design anything, it's a very different story (as DrL's link shows!) 14:06
@DrLemming Now, again, this is not anyone's fault: players are just getting the highest scores possible. This is mostly something we need to continue improving on our end. But it's worth reiterating what we're looking for, in any case. 14:06
@DrLemming Flat vs. curved isn't an issue; in fact, we'd love to see diversity there; a mix is great. :) 14:07
@DrLemming Okay, here's a really cool one: 14:07
eag111 Anyone like minecraft? 14:07
@DrLemming 14:07
auntdeen2 eag111 - this is a science chat 14:07
@katfish Hey eag, you're in a Scientist Chat right now 14:07
eag111 Oh, sorry 14:08
CFC sacked aromatics, looks good 14:08
CFC *stacked 14:08
@katfish No worries, eag. :) 14:08
Aotearoa wow nice design 14:08
@DrLemming I like this one for a number of reasons; stacked aromatics are great (especially when not solvent exposed) and the secondary structure content is high (it's not just spaghetti) - but most importantly, specific to this puzzle, the catalyst is buried in the proportionally large core, and it has a nice H-bond to it, from a histidine. :) 14:08
brow42 DrLemming, your filters HATE histidine for some reason. 14:09
@DrLemming There's no guarantee it will work, but this is a design we'll probably make (though in this case it's ultimately up to our collaborator, since she has to make these in her lab. The catalyst will oxidize in air if not handled properly, so we can't deal with it here.) 14:09
markm457IRC DrL - we frequently have more interesting, lower scoring folds in other tracks - I hope you also see those, not just credit best solution 14:09
@DrLemming Hmm... histidine hate? Sad... I'll look into that. I know they have low secondary structure propensity, so they're going to be better favored in loops vs. sheets or helices... 14:10
auntdeen2 mark - that is an excellent point 14:10
@DrLemming @markm457: we do tend to look at some of the lower-scoring stuff, but we are working on a system where players can flag interesting-but-lower-scoring structures so we're SURE to look at them. 14:10
Aotearoa alchemists or whitchcraft. burn them all. :-P j/k wow this is amazing stuff guys, thanks for sharing. 14:10
@DrLemming Because to be honest, there's no guarantee that we'll find an interesting lower-scoring structure - even though we do look at most solutions. 14:10
Chana I do that often in the name of shared to self solutions, remark they are must see 14:10
@DrLemming Which is why we're going to be implementing some sort of flagging, where you can highlight neat structures for us. :) Speaking for myself at least, I love looking at fun structures; even if they aren't viable as-is they can be inspiring. 14:10
MurloW except on this account, sorry multiple clients open. 14:10
firejuggler I like the idea of flagging your interesting structure.... but should you be able to flag yourself? 14:10
@DrLemming I think so. To be honest we don't yet know how we'll implement it. 14:10
@DrLemming Okay, David is here. :) 14:14
@DavidBaker Hello everybody! 14:14
MurloW if u make it a group-only feature you might miss out on great stuff! 14:14
@betahelix David Baker will answer the meta-helix question 14:14
firejuggler Hey 14:14
@DavidBaker I was excited when I saw the last set of design solutions! 14:15
@DavidBaker Some of them looked like designs I'm working on myself. 14:15
auntdeen2 :-) 14:15
auntdeen2 that's what we all want to hear 14:15
@DavidBaker We are interested in many different types of designs, those with mainly helices, those with mainly strands, and those that have both 14:15
@DavidBaker For example, some of the twisted helix designs resemble parts of naturally occuring proteins 14:15
steveB The twisted helix is formed automatically (in my experience) by the foldit programme. If you start with parallel helices, mutate then wiggle they end up wtisted 14:15
frood66 for sure 14:20
@DavidBaker The top beta solution resembles the structure of an amyloid forming protein-alpha beta crystallin 14:21
@betahelix (which was the very top-scoring Fold design for that puzzle) 14:21
brow42 can design be combined with exploration? Is there a bandwidth issue with having new exploration puzzles? 14:22
@DavidBaker we've talked about doing this-giving rewards for new design topologies. it is just a matter of figuring out how to balance diversity with score 14:23
MurloW something different though, will the buddy system be brought to life? 14:23
firejuggler design and exploration? that might end in meta-mega elix 14:23
firejuggler *helix 14:23
@DavidBaker I'm very interested in the symmetric oligomer designs, as these could form the basis for a whole new class of materials 14:23
@betahelix @murloW that question will have to be for another day... our time is almost up for today's Scientist Chat 14:23
firejuggler sorry, oligomer, word too big for me 14:24
@DavidBaker sorry-oligomer means a protein made out of multiple chains. like the trimer and tetramer puzzles 14:24
firejuggler ah thanks 14:24
@DavidBaker think of an icosohedron-it can be made by putting together trimers and pentamers 14:24
brow42 Feedback has a mechanism for asking science questions: Question-Biochemistry. I tried that once but didn't get a response. Instead of bringing them too science chat, would you be willing to check those questions? 14:26
@DrLemming 14:26
@betahelix 14:26
firejuggler icpsahedron is basically a soccerball 14:26
alwen made of pentagons & hexagons 14:26
@DrLemming @ brow42: I've just noticed your questions that you posted, and I'm planning on addressing them on the Foldit page; sorry there wasn't time here. They're very in-depth and thoughtful. 14:27
brow42 But as a continuing interaction... 14:27
@DavidBaker we will be testing your designs very soon-should be very exciting! 14:27
@DavidBaker and we should soon have speedups for the filters 14:27
brow42 Feedback doesn't work if nobody is reading it. 14:27
@betahelix brow42's questions here: 14:28
@betahelix 14:28
auntdeen2 and - can we get you back for another science chat soon - maybe next month? 14:28
@DavidBaker definitely! 14:28
@betahelix Are there any last questions for David Baker? 14:28
@betahelix hopefully by next month we'll have the slow filters issue resolved :-) 14:28
@DavidBaker thanks everybody! 14:29
CFC no, thank you :) 14:29
grampsIRC ty for info :-) 14:29
frood66 thankyou 14:29
marie_s thanks 14:29
firejuggler David: off topic : do you play other videogame? 14:29
steveB thanks 14:29
@betahelix we are actually planning another Scientist Chat next Tuesday at 2pm PT! 14:30
@betahelix With the Scientist who is working on the Sepsis puzzles :-) 14:30
utaca thanks 14:30
dflear that will be sweet 14:30
alwen Oh, that's cool 14:30
@betahelix we'll post details of that one soon, along with the next Sepsis puzzle... 14:30
auntdeen2 excellent :-) 14:30
@katfish Yep, I'll make a post about it shortly 14:31
@katfish So mark your calendars! 14:31
@katfish I'll also make a reminder post the day of just in case ;) 14:31
@betahelix Thank you all again for joining us today, and thanks again for all your hard work! 14:31
@betahelix Keep up the great folding!!! 14:31
alwen Good luck with the new server. 14:31
@betahelix :-) 14:31
@katfish Thanks, alwen! 14:31
utaca It's for fun, work is something different 14:32
@betahelix thanks again for all your hard fun! ;-) 14:32
alwen I can quit folding any time I want. 14:32
@katfish Thanks everyone for joining! Transcript will be up soon on the website. 14:32
@betahelix bye gang... 14:32
eromana Thank You All 14:32
steveB bye 14:32

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