We always look forward to chatting with the community, so here's your opportunity to get those science questions in so you can get answers. Please note, questions submitted immediately prior to the chat may or may not make it into the final question list, so the earlier the better!
Science chats are designed specifically to get assistance with scientific concepts (specifically as they relate to Foldit), discuss recent puzzles and timely topics, and get updates from the team. As always, suggestions should be placed in the forum, bug reports in the feedback area.
The Date: 22 March 2016 (Tuesday)
The location: #veteran, IRC (Get help with chat here.)
The Time: 2100-2200 (or so, but the official chat ends after an hour) GMT/UTC (aka 1400-1500 PDT, aka UTC-7)
The Time Zone Converter: Right this way!
I’ve noticed recently - maybe I have been blind b4 to this……why do I get voids shown on the outside of the protein when all local segs are hydrophiles? Anyone?
Np doubt there is an explanation - but it is eluding me
Do your mutate tool take into account the probability of concurrence of specific AAs in general (probability in nature) and/or for specific SS (preference for helix etc)?
I ask this because you are adding filters "against" several AAs that are over-represented in our solutions.
We solve this by hand mutate and/or recipes that mutate one by one while avoiding to use the mutate tool.
I suppose that, for us players, the initial state influences the final result when mutating a first design.
For example, if I start with all isoleucine then mutate all (all other thinks equal), I suppose that I would get a final different result than if I started with all lisine.
If I mutate one by one on random order, I'd have a different final result than mutating from seg 1 to n.
Question 1: is there any known generic "path" in nature or is it completely random and independent from context? thus DNA codes for a "nature selected" protein on a deterministic way independent from the context. Mutations are simply random and the natural selection does the job of retaining the useful ones.
Question 2: For anti bodies, how does the nature work? does it try mutating existing antibodies until it finds a mutation that works? (then we would find a lot of "waste" in blood). Or does it "recognize" a virus protein (as we human do on the models given to us), identifying possible weaknesses, THEN sythetizing a "deterministic" antobody, this with limited waste "mutations"?
Do you still record script use?
-or succession of commands or actions used for a top solution?
-are the scripts still of any help for Roseta algorythm ?
I will not be able to be at the science chat, but pls answer this one.
The Rama plot is used for all kind of amino acids. Are there significant differences when you look at the Rama plots of the individual amino acids? And would it not be better to be able to see the Rama plot of a specific acid?
What happened with the series of Marburg binders? Did you make use of the solutions in any way? (Puzzles 1073, 1108, 1112, 1144)
What's the status of the publication which used one of foldit's VEGF solutions? (Puzzles 1012, 1016, 1067)
Is there any news you can share about the UMich challenge? It doesn't have to be new news (from the latest puzzle); we would still like to hear the old news (how we did compared to the undergrads). (Puzzles 1152, 1193)
Thanks!
I agree with everything Susume says above, and in general feel there is an urgent need for more feedback on puzzle results, even if negative.
What is the auto structures tool based on - is it phi and psi angles? If not, could it be made to use phi and psi angles so it would show us what the rama plot shows (which residues are in a good SS shape for that aa and which are not)?
I'd like to know whether the results from the abeta binder contest (which I ahared with you a while ago) are being used to improve models and whether in general it would make sense to try and improve that model. If it would, how about an all-hands version of that, based on the contest ?
Would it make sense to allow Rama Map functionality in every puzzle so we can learn to use it better (or find new uses for it) ?
