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Joined: 02/24/2011
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Elevator pitch summary: what are the chunks in the stuff we see?

http://www.vimeo.com/21290870

phi16 and I have been talking about some ideas - intermediate levels of protein structure they were apparent in the structure in 405, the bottle and cork. in the above one can see evocative structures too, the grip. None of the following is Phi's fault unless it's good in which case he deserves credit.

segment by segment solutions scale like n^m. nasty big. need to attack the combinatorial problem. make lumps. hierarchical aggregations. In the military they call it the articulation of force - squads, platoons, companies, battalions, regiments, divisions, corps, armies. The army thinks it is real important to have the chain of command.

So I wonder (phi too I think) what are the useful middle level structural elements. Our Legos. Because Legos promise a faster search.

Helices, sheets, loops, but also bottles and walls and axes, and grips. Aggregation reduces the complexity of the search. Better 10 items of 5 units each than 50 units of 1. That's my strategy and I'm sticking to it. DNA cubes.

writing about foldit in my wiki
let me know if it bugs you.
http://wut.wikia.com/wiki/Foldit_Home

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons