I had a short chat with David Baker and grad student Javier Castellanos this morning. We discussed new visualizatoins options for foldit, design aids, and ways to facilitate more communication between the community and techical staff.
David once again commended players for their interesting designs and how much they have improved under the filters, and hopes they will become much less painful soon as the filter effects are moved into the score function itself. I didn't have any specific comment about the filters right now, but I'm sure many of you have plenty to say!
I had a suggestion for the recent sepsis puzzle (and other ligand bonding puzzles). I noted that a good solution seemed to require 1) the hydrophobic core remain covered, 2) we need increased bonding to the ligand, and 3) we need a nice stiff secondary structure to hold the bonding residues in place. We need more residues available to do all three (the last two puzzles were +10, then +6). Also, I've noticed that the last locked residue would leave the protein pointing in an 'inconvenient' direction, and more should be unlocked farther back.
The Baker lab recently did a study on how groups of strands and helices folded, and made a list of rules summarizing them. They then designed entirely artificial combinations following these rules, ran them through Rosetta@Home, and then actually synthesized them in the lab and measured their structure, and found that the designed proteins folded as designed.
These rules answer simple questions: should this strand turn left-right; should this helix go over-under the sheet; should the helix go left-right. The answer is always "both" but short connecting loops prefer one way, then prefer the other as they get longer.
Since the Baker lab wants us to not just make interesting designs, but designs that fold as predicted, I asked if these rules could be turned into simple English, along with visualization aids (more below), so that players could make more stable designs. Javier, who does design work, could help with this.
These rules would also make de novo folding less daunting. Perhaps, if the visualization was kept informative, not suggestive, it would preserve diversity.
I asked David if we could have Foldit provide more information to the player. For example, when I started as a new player, I would see that a segment has a bad backbone score, but I wouldn't know why. Eventually I learned that if you left a script to rebuild that segment, eventually it would get fixed. There are many sorts of twists the backbone can make that are invisible. Foldit could communicate more information about the angles, and highlight flipped segments (cis bonds).
I emphasized that whatever visualization is added, it should not be color based. Now that I think if it, it should not add clutter, either. Perhaps it draws the extra visualization only when a key is pressed.
One very easy visualization to add is to simply indicate the direction of the strands (which are drawn as arrows in pyMol but are unmarked in Foldit).
David Baker would like this chat to be the revival of the player-dev-scientist chat. ( http://fold.it/portal/node/992501 ) He would like the community to participate in the bi-weekly skype meetings. The group leaders and expert players could take the comments of the community, consolidate them, and translate them (for example, turning what a new players sees happening into what foldit is actually doing). The scientists can't really monitor the forums. Bug reports are immediately looked at by the devs, but questions and suggestions aren't necessarily passed along.
I think a good start would be: the expert players consolidated the questions and suggestions (not bugs) in the feedback, the group leaders contribute what was being said in group chat, and the community in general use the existing voting mechanism on the questions and suggestions. This could be presented as a consolidated posting or in Skype. I prefer written communication, but David likes Skype, and with Skype you know they've gotten our feedback and discussed it.
Please post your thoughts on how we can organize ourselves to communicate more directly and regularly. Also, what visualizations you'd like to see, or if you think design rules is a horrible idea, post below!