Developer Chat

Thu, 04/19/2012
@betahelix Hi everyone! We'll be starting the Double Scientist Chat in ~half an hour! 14:05
thealbatross awesome! 14:05
thealbatross ...I'm going to have to miss it though :( 14:06
frood66 i do not put the game down here - only point out the obvious 14:06
@betahelix I am about to post the new Flu Puzzle so you can play around it for 30 minutes before the Scientist Chat: 14:07
@betahelix http://fold.it/portal/node/992416 14:07
MEFreed Hi beta - yay new puzzle! 14:07
thealbatross awesome! 14:07
frood66 hi beta 14:07
@betahelix Hi gang! 14:07
@betahelix wait for it.... 14:07
frood66 not really 14:07
@betahelix ... 14:08
frood66 other puzzles end soon 14:08
@betahelix you still have 2 hours for 542, plenty of time ;-) 14:08
@mimi2 there speaks the non player :) 14:09
frood66 and little machines allow little extra 14:09
thealbatross 542 is a tough one 14:09
thealbatross I found a good alignment, but sealing those cutpoints is pretty tricky 14:09
frood66 beta - guess u will have to be 'beta' than that 14:10
frood66 for the 'little guys' - 2 hrs is a lot 14:11
@betahelix hahahaha... I was totally being facetious! 14:13
thealbatross heh heh 14:13
thealbatross I'm going to try out that new one... 14:13
kristis ? 14:13
kristis hey 14:13
frood66 i know what facetious means 14:13
kristis why everything is locked 14:14
@mimi2 we know - but you gave us the opportunity 14:14
frood66 not a good idea - i suggest 14:14
frood66 hi mimi 14:15
@mimi2 greetings and salutations 14:15
frood66 :) 14:15
@betahelix I know how hard 542 is, we will repost it soon with the "best alignment" and the native as a guide 14:17
thealbatross Ooooh.... 14:17
thealbatross good plan 14:17
@betahelix anyway... I will let you work hard on that (and check out the new Flu puzzle, 546) and I'll be back for the Scientist Chat in 15 minutes! 14:17
frood66 beta: u underestimate 14:17
@betahelix never! ;-) 14:18
MEFreed Quick - while beta is here, all in favor of hammer tool say Aye! 14:18
MEFreed :) 14:18
frood66 air hammer! 14:18
MEFreed (Dislike this protien very much) 14:18
@betahelix you mean the scissor tool? 14:18
frood66 thought u were gone lol 14:19
MEFreed Nope. Hammer. To murder the protien more violently than setting ci to 0. 14:19
thealbatross (heh heh) 14:19
frood66 nahhh - TNT 14:19
@betahelix hahahahaha... duly noted. see you soon. bye! 14:19
thealbatross later 14:19
frood66 well i'm still smiley 14:20
frood66 guess it's my problem 14:20
harp hi frood, hammer would be a most interesting addition to the tool kit, lol. I am in favor of it :-) 14:22
MEFreed It would be a nice way to talke out anger at a protoine. 14:23
harp with a caution: may cause major damage to computer xD 14:24
MEFreed Still probably less than a real hammer :) 14:25
frood66 hey harp 14:26
harp Would feel pretty good sometimes lol 14:26
harp hey how are you? 14:27
frood66 smiley now 14:27
frood66 *snigger* 14:27
harp sure about that ? 14:27
frood66 no happy thx harp 14:27
frood66 rewind.... 14:28
mottiger SCIENCE CHAT 14:28
frood66 happy - thx harp 14:28
harp k 14:28
frood66 2 mins mott 14:28
beta_helix Hi everybody! 14:31
MEFreed Hi beta! 14:31
frood66 hey 14:31
beta_helix Please welcome DavidLa from the Baker Lab 14:31
davidla hello 14:32
silverberg hello 14:32
MEFreed hi davidla! 14:32
@auntdeen2 welcome, davidla 14:32
beta_helix He's working on the new way to fight to Flu: 14:32
mottiger hey david 14:32
beta_helix http://fold.it/portal/node/992416 14:32
frood66 hey hey 14:32
twisted1 hi davidla hi all folders 14:33
beta_helix We just posted DavidLa's new puzzle if you have any specific questions about it. 14:33
beta_helix (Puzzle 546) 14:34
mottiger strange, i can log into all three puzzles 14:34
spmm2 is there a reason for the piece being bent or does it just come that way? 14:35
mottiger <15 <150 and open 14:35
@auntdeen2 I have a question... is it better to have bonds to the frozen piece or not? It seems that highest scoring solutions on flu puzzles are not the ones with the most bonds 14:36
davidla hi spmm2 14:36
frood66 davidla: now would be qa god time to tell us yr thoughts 14:36
spmm2 hi DrL 14:36
davidla that was the initial structure we started with 14:36
davidla but you should feel free to change it in anyway you like 14:36
spmm2 tx 14:37
frood66 so the initial structure is of no value? 14:37
beta_helix @mottiger that is strange, I see that as well (will bring it up to the devs) 14:38
davidla auntdeen, you can have bonds to the initial structure if you like 14:38
davidla definitely try whatever you think would work best 14:38
@auntdeen2 yes - but exactly is it that you are looking for? 14:39
Lazarus-uk yes, beta, there is a feedback posted about <15 and <150 14:39
mottiger it's another mutate GAB puzzle 14:39
spmm2 having moveable sidechains in the socket area is great 14:39
@auntdeen2 sorry - what exactly? 14:39
mottiger if the sidechains in the virus protein are flexible, don't we change the backbone then? 14:40
frood66 well i got my answer 14:40
davidla auntdeen2, we don't have any assumptions what this small 3 amino acid should look like 14:40
davidla just as long as it can fit in the flu viruses pocket, and can hold on tightly, that would be great. :) 14:40
@auntdeen2 thanks, davidla - but can you define "hold on tightly"? 14:40
@MikeCassidyToo Yes i can also play all three 546s 14:41
beta_helix @Lazarus thanks, I assigned it 14:41
frood66 so this is no different to recent puzzles? 14:41
beta_helix @Mike we'll get that fixed soon, I can manually change it but I want the devs to diagnose the issue first! 14:41
davidla mottiger and frood66: you can definitely change the backbone 14:42
frood66 so? 14:43
davidla we want you to change the backbone 14:43
beta_helix but not the backbone of the virus ;-) 14:43
mottiger nope i mean on the locked virus protein 14:43
davidla oh, you cannot change the backbone of the virus 14:43
mottiger the sidechains are moving 14:43
frood66 thankyou - some direction 14:43
mottiger but the backbone is fixed 14:43
davidla we assume that will stay the same 14:43
mottiger which is very nice i think but isn't the danger that we damage the protein too much? well wait, that's what we want 14:44
beta_helix @spmm we figured you would all enjoy having some flexible sidechains on the virus :-) 14:44
frood66 please beta 14:45
Susume2 I wish bonds to the virus could count for more points than bonds just on the ligand 14:45
spmm2 :D - roughly how big is the rest of the small piece or will that vary 14:45
Psych0Active absolutly! 14:46
davidla we are letting you change the residue orientations to help make the 3 amino acid piece fit better 14:46
beta_helix @susume that is something we could probably add in future puzzles. 14:47
frood66 so u r making it easy? 14:47
davidla spmm, so what we wan to do is take this 3 amino acid piece and transplant it on to another small protein that would be 40-250 amino acids long 14:48
mottiger what are the plans with the already produced data of foldit? do we have chance to see another round of the flu puzzle with data of us? and how will that look? 14:48
beta_helix @frood66 no, we just wanted to start by giving you more freedom before restricting you too much. In previous Flu Puzzles we started VERY constrained and then relaxed those parameters in future puzzles. We wanted to go the other way this time. That is why the constraint is very far on this puzzle. 14:48
davidla we don't know the exact protein we would like to place it on just yet, it depends on the type of solutions you guys can come up with. 14:49
mottiger do you compare our solutions with already known proteins? and then try to modify it or is it a complete new design? 14:50
TimovdL How valid is the assumption that the backbone of the virus will stay fixed when the blocker is there? 14:50
frood66 would have helped if u had said so in the first place beta - many have been here longer than I. think u owe ythem that 14:51
davidla mottiger: we would like to compare your new solutions with known solutions, yes 14:51
beta_helix @mottiger I'm getting one of the Scientists from a previous puzzle to come and answer your question :-) 14:51
davidla i'm optimistic and very excited to see all the possibilities there are 14:52
frood66 Hmmmm 14:52
Susume2 Any chance of designing a protein that mimics the bit of the human cell that the virus bnids to? 14:53
mottiger yeah i can understand that excitement but with time it is getting a bit boring just grinding with 3 segments, but i think we need to build a solid base to make a nice protein later on 14:53
beta_helix EvdH can answer that, mottiger 14:53
@EvdH Hi guys! 14:53
frood66 hi 14:54
Psych0Active Hi :) 14:54
@MikeCassidyToo hi EvdH 14:54
davidla TimovdL, from all viral structures of this virus that we know of, the backbone remain the same either bound or unbound 14:54
TimovdL tx 14:55
spmm2 HI EvdH - any early results from the earlier puzzles 14:55
beta_helix The blogpost has a great link to a diagram showing the Flu Virus: 14:55
beta_helix http://fold.it/portal/node/992416 14:55
@EvdH Well mottiger, these 3 residues actually make up the most important part of the binding motif towards the protein. So they may look as only 3 small residues but they have a huge impact. We are going to graft these three residues onto a larger protein, so we can really create a protein-protein interaction 14:55
davidla Susume2: yes, essentially, this is the first step towards mimicking the human cell receptor 14:56
Psych0Active Wow! :) 14:56
@EvdH sure spmm2! Actually I'm currently analyzing all of the 60,000 solutions all the Foldit players came up with. 14:56
@EvdH But it's not as straightforward as only looking at the top10 highest scoring models ;) 14:57
mottiger and can we see any of these exciting binders someday? 14:57
Psych0Active How so? 14:57
frood66 no kidding 14:57
@auntdeen2 that was my earlier question... how are you defining "hold tightly"? 14:58
@EvdH That is indeed the ultimate goal mottiger :) 14:58
@auntdeen2 are backbone bonds better than sidechain bonds? 14:58
mottiger like gallery mode or so, you can load several solutions you think they are really promising, without being able to touch them, just like in a museum 14:58
frood66 aunty - nice - i want to know that 14:59
beta_helix we love the backbone bonds! 14:59
beta_helix but we don't know if there score better 14:59
davidla auntdeen2: hold tightly would be number of hbonds you can make with the 3 amino acids you select 14:59
davidla also, don't forget the pocket you are targetting is hydrophobic 15:00
@auntdeen2 we do too, lol - but are better than sidechain bonds for your purposes? 15:00
davidla so putting hydrophobic type residues in the pocket would be very nice 15:00
frood66 we await an answer 15:00
infjamc How can you prevent abuses such as poly-tryptophan, though? 15:00
beta_helix yes, because they are more likely to be there (since the Flu can mutate its sidechains a lot more easily) 15:01
@auntdeen2 I do ask simply because our software doesn't seem to value the bonds as much as it seems it should 15:01
beta_helix @infjamc we're using a newer score function that seems to be working well. 15:01
frood66 yea yea yea 15:01
gdnskye so the more the better - hbonds? 15:01
infjamc beta: does the new score function limit the effectiveness of the "four glutamates / four arginines" trick as well? 15:02
davidla gdnskye: yes 15:02
gdnskye thanks 15:02
frood66 guess we are all asking for a little guidance 15:03
mottiger hihi, we are doing science, there is no guide to it 15:03
spmm2 I quite like these small ones because they are flexible enought to just try lots of positions 15:03
frood66 that is simple mott - not what i said 15:04
spmm2 cheer up frood 15:04
@mimi2 always the arguement that if we don't know it isn't right we will be prepared to try the impossible 15:04
frood66 never so happy spmm 15:04
beta_helix @frood please restate your answer (there are a lot of questions!) 15:04
frood66 yes mimi 15:04
frood66 beta: i had no answer 15:05
beta_helix restate your question (sorry... many people talking in this room!) :-) 15:05
beta_helix @infjamc yes, that should also have been fixed. We haven't seen these issues crop up in any of the top solutions recently! 15:07
frood66 there is , perhaps, the problem - be straight - these lab rats may have a better chance 15:07
beta_helix @frood I am very sorry, but I still don't understand your question. Do you have something you want DavidLa to answer before he has to leave? 15:08
frood66 not sure i did - that must be yr imagination 15:08
beta_helix Anyone have any last questions for DavidLa before we move on to the new Symmetry Puzzles? (I will post it in Gallery Mode) 15:08
@auntdeen2 please, devs - I am still looking for the answer to your definition of "hold tight" 15:09
spmm2 DrL - can we assume that there will be extensions from both ends of the 3 a piece ? 15:09
Susume2 is there anything besides hydrogen bonds that helps the protein stikc to the virus? 15:09
beta_helix @frood, ok good! I was afraid we didn't answer your question because we read "we await an answer" 15:09
frood66 it is an old navy term 15:09
aSuAhSaD i just want to say that i enjoy this prograsmm very much but now i have to go to learn tomorrow what i do in this prog 15:09
davidla ok, hold tight means: more hydrogen bonds of the tripeptide to the virus 15:09
beta_helix @spmm I'll post the puzzle in Gallery Mode so you can try it out! 15:10
davidla also, more hydrophobic contacts 15:10
@auntdeen2 on puzzle 543 atm - I am at r18 with 4 bonds - 2 to backbone, a 5th is the small piece backbone to itself 15:10
davidla to hydrophobic type residues of the virus 15:10
spmm2 cool thanks 15:10
mottiger my current rank 8 flu2 has just two hbonds 15:10
mottiger i don't like the solution but it seems to score well 15:10
@marie_s hold tight is also : if you try to get itout, it doesnt want? 15:10
@auntdeen2 but mott on my team has a higher score with just 2 bonds to the frozen peice 15:11
frood66 hold tight mott 15:11
@auntdeen2 so I am wondering 15:11
davidla if you are doing hydrophobic packing, you don't need hbonds 15:11
davidla btw 15:11
@auntdeen2 so the bonds do not matter then? 15:11
frood66 why is this not in the puzzle notes? 15:12
@MikeCassidyToo In the AD all we can do is through the score if that is leading to the wrong place they will modify the scoring 15:12
@auntdeen2 thank you, that does answer (but really makes me wonder then what our gauge is) 15:12
davidla for hydrophobic residues, there are no side chain hbonds 15:12
beta_helix @auntdeen sadly your gauge is the score function (as you well know) 15:12
frood66 how much time would u guys like us to waste? 15:12
Susume2 beta does the hydrophobic packing show up inthe packing component of the score? 15:13
@CFC easy frood 15:13
frood66 cfc: explain? 15:13
frood66 that was a fair comment 15:13
frood66 tell me it was not 15:14
davidla one thing this is leading to is molecular mimicry 15:14
davidla the virus you are targetting now binds to a known ligand, called sialic acid 15:14
davidla one thing i have in mind the future is to put sialic acid as part of this flu puzzle, overlay it so that you can put residues int to try to mimick it 15:15
Susume2 that would be very cool 15:15
beta_helix @frood I would say: play as long as you enjoy it. Don't waste any time on Foldit once it makes you cranky :-) 15:16
phat865 Hi 15:16
davidla that would be really awesome. but for this puzzle, we wanted to see if you guys can beat sialic acid 15:16
beta_helix Ok everyone... it's time to let DavidLa get back to work! 15:16
@marie_s thanks davodla 15:16
harp Thanks David 15:16
davidla if you guys can find something that would bind more tightly than the native receptor, that would be incredible 15:16
Susume2 thank you DavidLa 15:16
davidla judging by the amino acids in this virus's pocket 15:17
davidla i really believe that there are lots of great opportunities for this 15:17
gdnskye thanks davidla 15:17
mottiger this is also work beta ;) 15:17
beta_helix I have posted DrLemming's puzzle in Gallery Mode, here is his general blogpost: 15:17
beta_helix http://fold.it/portal/node/991246 15:17
@MikeCassidyToo TY davidla and beta_helix 15:17
davidla thanks guys! 15:17
TheGUmmer ty 15:17
spmm2 thanks i always wondered why those orange packed areas scored so well without visible clues of bonds 15:17
davidla i can't wait to see what you guys come up with 15:18
beta_helix @mott with you guys doing the hard work! :-) 15:18
DrLemming Hey everyone! DrLemming here. New puzzle to check out in gallery mode! It's a mostly-free-form symmetry/design puzzle. Let me know if you have questions! 15:18
TheGUmmer drat missed it 15:19
mottiger well it isn't really work beta, you can not make any thoughts about what should i put there, my point is just let your mutate script run and hope for the best 15:19
mottiger it is a dimer, not a trimer 15:19
DrLemming Ah, does the description say trimer? Whoops. Let me check it out... 15:19
mottiger i have trimer in mind 15:20
beta_helix @TheGUmmer you still get the second half of the Scientist Chat :-) 15:20
DrLemming Ah, gotcha. That's an old blog post for a related puzzle. 15:20
mottiger ah okay 15:20
DrLemming But it's the exact same idea: taking an existing trimer or dimer and expanding it so we can do more with it. 15:20
TheGUmmer o 15:20
mottiger and what do you plan to do with it? 15:21
DrLemming Okay folks, I might post a long-form puzzle description here. Large text block incoming! 15:21
DrLemming Structured dimeric and trimeric peptides are great starting points for a major bioengineering challenge. Specifically, they can be used as building blocks for designing useful, rigid assemblies of proteins, like crystals and nanocages. The smallest such starting point for this kind of design is an ...WXCXW... motif, which forms a tiny structured homodimer: 15:21
beta_helix @TheGUmmer (and anyone just joining): check out the new puzzle in Gallery Mode and ask DrLemming any questions you have about it! 15:21
DrLemming a short beta sheet stabilized by a cross-strand disulfide bond and two tryptophan/tryptophan interactions. The only problem: this motif is so tiny, it is difficult to do anything with; it needs to be larger but retain rigidity. Otherwise anything goes: beta sheets, alpha helix docking, rigid loops, you name it. We've given you 20 extra residues to play with 15:21
DrLemming @mottiger: I'm trying to assemble small dimers and trimers into nanocages, rigid crystals, and other interesting scaffolds. Basically, I'm trying to make a really useful lego piece. :) 15:22
DrLemming So it could be used for a number of things. 15:22
silverberg Is it bad that I have no idea what you are talking about, and that is not an insult. I just play the game. 15:22
silverberg Like these extra residues. What do I do with them? 15:23
mottiger name it please, why are we interested in nanocages, maybe drug delivery? 15:23
beta_helix @silverberg don't worry... you just joined us in the middle of a Scientist Chat. No more big blocks of text, we promise! :-P 15:23
silverberg I was here at the beginning. 15:24
frood66 thx lemming - at least u tell us what u r aiming for 15:24
TheGUmmer take notes, there will be a quiz later 15:24
frood66 haha 15:24
silverberg I read what you type, but I do not have the understanding (yet) to er.. understand. 15:24
@auntdeen2 (I know I will fail :-P ) 15:24
DrLemming @mottiger: drug delivery is one interesting application, but something I'm really excited about is using nanocages to template metal nanoparticle assembly. 15:24
frood66 aunty - that is not the attitude 15:25
@auntdeen2 ;-) 15:25
DrLemming But, in a general sense, I just want you all to design some dimers that look really cool. That's the... secondary objective. :) 15:25
beta_helix @silverberg for the Flu puzzle, there is a cool diagram if you click on the link in the blog: 15:25
beta_helix http://fold.it/portal/node/992416 15:25
DrLemming In terms of design: just have fun! Anything low-energy. But please try to preserve the orientation of the frozen residues. (It's possible to break them apart, even though they're frozen.) 15:26
silverberg thanks. But no worries, it is a learning curve for me, and I like a challenge. 15:26
spmm2 metal naoparticles - is that similar to the work being done using gold to identify target areas 15:26
beta_helix @silverberg that's what I love to hear! 15:27
mottiger so if you really interested in these cages, can you somehow force us to do something in that direction? 15:27
silverberg Yay! 15:27
frood66 DrL - thx - nice to have direction 15:27
DrLemming @spmm2: sort-of. That's a really good biological application of metal nanoparticles, but I'm just interested in being able to make nanoparticles of a very specific size; not thinking so far ahead that I'm considering new applications. 15:28
@marie_s the 2 frozen part have to stay where they are ? 15:28
spmm2 tx 15:29
DrLemming @frood66: I can provide specific suggestions if you'd like. A large beta sheet should probably work (making a hairpin using the central strand as one of the sheets). 15:29
DrLemming @frood66: it's something to try, anyway, if you're after specifics. 15:29
DrLemming But in general, I want this to stay very free-form. 15:30
frood66 DrL: well it mght help - thx 15:30
DrLemming @marie_s: great question! Yes, the frozen stuff should stay in place. However, some of the frozen residues can be mutated. 15:30
@marie_s they are not frozen one near the other 15:31
TheGUmmer IMAGE: http://fold.it/portal/files/chatimg/irc_12518_1334874694.png 15:31
spmm2 oh wow a mutating dimer - hours of fun :D 15:31
DrLemming @marie_s: It's possible to pull the central beta sheet apart, but this will probably result in very poor energies.... 15:31
@marie_s ok we have to try not to explose the pair 15:32
beta_helix @spmm that's what we thought as well! 15:32
TheGUmmer everyy other seg on the sheets has its structure locked 15:32
DrLemming OH, the secondary structure assignment isn't frozen; gotcha. Feel free to change the designation to loop if you'd like; it could help mark which residues are fully frozen, and which have sidechains that can be mutated. 15:33
mottiger may it is usefull in a first stage to completly freeze these two sheets 15:34
DrLemming @TheGUmmer: correct. All segments that face "up" are locked (two tryptophans and a cysteine on each strand) , while "down" is not sidechain-locked. 15:34
frood66 DrL: so sneaky 15:34
@marie_s they are not, we can split the pair 15:34
DrLemming @mottiger: technically the backbone is frozen for all 5 residues, but unfortunately we haven't been able to add cross-interface constraints to keep those 5 frozen residues in perfect alignment with each other. 15:35
frood66 i am looking for a bigger machine 15:35
@marie_s ah ok 15:35
DrLemming @mottiger: we're working on a fix, but we may have to launch the puzzle as-is. Hopefully not a major issue; when the frozen strands are pulled apart, it shouldn't score as well. 15:36
mottiger you never know what we are able to create 15:36
frood66 oh boy 15:36
DrLemming @mottiger: indeed! :) Looking for some creative, low-energy designs. 15:37
beta_helix Are there any other questions for DrLemming? 15:37
DrLemming Design note: One side of the beta sheet has residues that can be mutated, so that players have the option of packing it against another chain. 15:38
DrLemming Oh, I should mention: I will actually be making at least one of these designs. 15:38
DrLemming One of the lowest energy designs. (Maybe not the very lowest, in case there's still an exploit we missed.) 15:39
frood66 terifican exploit? 15:39
spmm2 is it possible to have the shadow of the moveable piece a different colour to the frozen piece 15:39
mottiger what do you mean with making? synthesis? 15:39
frood66 eek - exploit? 15:39
DrLemming @mottiger: yes! Chemical synthesis (since it's so short) and then an NMR or X-ray structure, if it folds well. I might make more than one. 15:40
DrLemming And I'll let any players/designers know how it turns out, if I use theirs. :) 15:40
mottiger i always wanted a nmr of an own designed protein 15:41
frood66 fantastic 15:41
alwen lol, mott 15:41
spmm2 so for the dimer - there is no 'native''? 15:41
frood66 hey spmm 15:41
DrLemming @spmm2: good question; I'd have to ask the devs. That would be convenient! 15:41
DrLemming @spmm2: there is sort-of a native. Essentially, the frozen residues are taken from the native NMR structure. However, it's not in the PDB. 15:42
DrLemming @Just seven amino acids (XWXCXWX, where X can be anything) folds up into a very stable beta-sheet dimer. I'd like to see how we can add to that dimer. :) 15:43
spmm2 tx - q was really more of ├žloser to the native' vs top score 15:43
DrLemming (sry; @spmm2 for above post.) 15:43
@thomirc8 Is there an energy value (i.e. Foldit score) for the native that can be posted? 15:44
@thomirc8 either will do - we can convert ;-) 15:44
frood66 o golly 15:45
DrLemming @thomirc8: Ah, I see. The starting structure is effectively the native structure; the frozen residues are already optimized. So I don't really have an energy for you, other than what the puzzle starts with. Sry. 15:45
@thomirc8 no, that works - thanks 15:45
@thomirc8 and for the record beta (it came up last night), all puzzles are now scoring disulfide bonds, right? 15:46
mottiger so what are you doing now? waiting until we produce a nice solution and make coffee for the postdocs or have you other projects, may related to this onee? 15:46
frood66 steady mott 15:47
DrLemming @mottiger: PLENTY of other projects. :) (Spread between 3 labs!) Though making myself coffee does sound good. ;) 15:47
beta_helix @thom yep... disulfides should be all good from now on! 15:48
@thomirc8 thank you 15:48
DrLemming @mottiger: also, I'll be doing a re-run of this puzzle using an N-terminal extension instead of the current C-terminal extension. (Same 20 residue extended chain to play with, but on the opposite side.) 15:48
DrLemming @mottiger: But I'll see how it goes first. (There may be more issues to address, etc.) 15:48
mottiger so you are playing yourself? 15:49
frood66 r u being me mot? 15:49
mottiger i'm just curious about what is behind the scene 15:49
beta_helix Five more minutes left in the Scientist Chat everybody... 15:49
DrLemming @mottiger: yep. I use Foldit for design regularly; it's really handy. :) 15:50
beta_helix most of the people in David's Lab working on design use Foldit on a daily basis! 15:50
frood66 mott: yes - been there - drop it - message me? 15:50
mottiger handfolding or also using scripts? 15:50
spmm2 I wanted to ask about how the scientists visualised proteins and interactions or if they did at all 15:50
DrLemming @mottiger: I have a few related designs that I like, but I want to wait until I get the results back before I synthesize or order peptides, because chances are a regular Foldit player will come up with something better! :D 15:50
mottiger then wouldn't be interesting let us work on already existing solutions? 15:51
spmm2 also as you have already answered that question - with the results anyalysis - what tools do you use to crunch the numbers 15:52
spmm2 and then visualise the results? 15:52
@thomirc8 it would also be be neat to see how you all use foldit vs. how we do it (such as view options) 15:52
mottiger minimal view options to have as much clients as possible ;) 15:53
frood66 mott: stop it 15:53
beta_helix @spmm EvdH can tell you how he analyzed Puzzle 539: 15:53
beta_helix http://fold.it/portal/node/992285 15:53
DrLemming @mottiger: I don't have any solutions that I feel good enough about to share right now; would prefer not to taint the imaginations of the players. :) 15:53
mottiger please drlemming, don't be ashamed ;) 15:53
DrLemming @mottiger: It's been tricky to design something that looked good, which is part of the reason that I chose this as a design puzzle. Very excited to see what players come up with! 15:54
@thomirc8 beta: would it make sense to have these gallery puzzles open to uploads? 15:54
frood66 mott 15:54
mottiger vote for permanent gallery view for puzzles where people can contribute their solutions if they want 15:54
beta_helix I think that's a great idea! 15:55
@EvdH @spmm2 for the Immuno design puzzle we first make use of filters which are based on some thresholds. For example, I first look which kinds of unique solutions exist, and I then select the top one. Next step is to calculate (in this particular case) the binding energy of the 3 residues with the big protein, so this gives a measure how tight the binding would be. 15:55
DrLemming @thomirc8: My fav. settings are: show all bonds, but not exposeds or voids by default, until I'm double-checking packing. I alternate between cartoon and all-atom stick, etc. 15:55
beta_helix @mottiger In fact, EvdH and I were just talking about posting some of his favorite 539 solutions into gallery mode 15:55
mottiger help me, what is 539 15:56
mottiger was 15:56
beta_helix http://fold.it/portal/node/992285 15:56
spmm2 being able to intereact with top solutions would be great much better than pictures 15:56
@EvdH Yep, I think it would be nice to give you guys a nice sneak preview of some cool solutions :) 15:56
DrLemming @thomirc8: but I think most folks in the Baker Lab have different fav. settings; depends on personal preference. I deal mostly with very small stuff, so I like to see as much info as possible; very cumbersome for larger proteins. 15:56
beta_helix @spmm of course! 15:56
mottiger a lot of people would be super interested in this 15:56
tokens Will the solutions we are making in the gallery puzzle now be saved and usable for when the puzzle comes up for real? 15:57
mottiger pictures in the wiki are nice, but looking into a protein deep and compare them can be fun too 15:57
tokens So the current work is not wasted 15:57
frood66 EvdH: enough now 15:57
beta_helix Any last questions for DrLemming? 15:57
harp that would be very interesting 15:57
frood66 beta: square this mess off 15:58
frood66 now would be good 15:58
mottiger when will the puzzle be posted? 15:58
beta_helix @frood66 I don't understand your comments... nobody is forcing you to take part of this chat. You can uncheck the Global Chat box if you are unhappy. 15:59
beta_helix @mott Probably early next week. 15:59
DrLemming @mottiger: very good question. I... am not 100% sure. Oh, nm, answered. :) 15:59
frood66 look back beta 15:59
DrLemming @mottiger: We will try to constrain the two frozen sections so they can't be yanked apart and destroyed... but no guarantees. :( 15:59
mottiger even if you can fix it, i'm sure someone will find a way to destroy it anyway *lol* 16:00
DrLemming @mottiger (symmetry is still in its infancy. There are some occasional... side-features... to address.) 16:00
spmm2 thanks for coming and answering questions - changing the colour of the shadow pieces would help me a t least 16:00
beta_helix @frood I am looking back and only seeing negative and rude comments from you, feel free to PM me if you want to discuss this further. 16:00
@marie_s I think we can try like this 16:00
spmm2 yes agree marie 16:00
DrLemming @mottiger: indeed! Foldit players are incredibly creative like that. ;) But I'd at least like to make it less fragile, if possible. We'll see. 16:01
beta_helix @spmm I'll bring that up at the Foldit meeting tomorrow 16:01
silverberg yes, thanks beta 16:01
beta_helix @marie great, that's why we wanted to double-check with all of you in gallery mode during the chat (so you could tell us if anything was wrong or confusing!) 16:01
beta_helix Ok gang, please thank EvdH and DrLemming for stopping by! 16:01
DrLemming @spmm&beta_helix Yeah! Should be a fairly simple fix: color change of shadow-symmetry partner vs. frozen. 16:01
@marie_s thnaks all 16:02
mottiger come back soon evdh and lemming 16:02
@auntdeen2 thanks, all :-) 16:02
@mimi2 thanks all very interesting 16:02
silverberg thank you EvdH and DrLemming 16:02
spmm2 beta before you dash off 16:02
DrLemming Thanks everyone! I'll try to address any more questions as they come up, once we post the puzzle! :) 16:02
beta_helix Thank you all for your hard work! 16:02
harp Thanks exciting stuff 16:02
frood66 thx 16:02
DrLemming Happy designing! 16:02
gdnskye yes thanks evdH and doc - was a great chat 16:02
@EvdH no problem, was interesting again :) 16:02
mottiger and i hope we can provide you some nice results, but please keep us informed what you are doing and present some of the intersting stuff 16:02

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