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Nicm25's picture
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Joined: 04/22/2020
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* this is survey for me as player, and results of your answers may be shared with certain developers.

hey guys,
I would love to hear from you guys who are playing lot with foldit.

I am working on whether it is possible to have computer solve ED puzzles.
and trying to provide a tool to automatically estimate poses from density.

and want to ask you...
'how would you feel if new tool was introduced for ED puzzles?'

do you not know what ED is? do you find it difficult to find density in these puzzles?
In future ED puzzles, would you like to modify proteins along with candidates suggested by machine?
do you still think that these will be competitive disincentive because you want to manually place them in density?

I think it actually depends on what the developers want, but I would also like to know what you think it would mean for players.
thanks for looking, please feel free to answer.

NinjaGreg's picture
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Joined: 05/21/2010
Groups: Go Science
New tool for ED puzzles

I'd welcome any new tools! I have a very hard time following the densities, so rely mostly on recipes. A new tool would be a nice addition!

horowsah's picture
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Joined: 03/17/2016
Groups: DU Proteins S20
New tool for ED puzzles

Just an FYI, we are working on new tools for ED- not sure how long they'll take to develop. Still, knowing what things players find hardest about ED is useful for us.

Joined: 09/24/2012
Groups: Go Science
tools and scripts

I tried to develop a walking tool following a Human recognized good position in the cloud, but it didn't work: evenu using the density points, the computer quick loose the right path in the cloud.

To find the starting point is the main problem that only human can curently solve. Any tool that would help to recognize aromatics in the cloud would be great. May be AI can do this job by using a lot of ED human solved "signatures" of aromatics.

jeff101's picture
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Joined: 04/20/2012
Groups: Go Science
Hoops and the recipe shiftit0:

I have posted many ideas for new ED Tools as Feedbacks 
on the Foldit site, but it doesn't hurt to mention some
of these again.

One idea is to create hoops in Foldit. Hoops would be a
bit like bands in that they affect the position of the
protein, but one big difference is that the protein could 
slide through a hoop like thread passing thru the eye of 
a needle. With hoops, we could designate a path for the
protein through the electron density cloud. Once the path
is established, we could pull on one end of the protein
to pull the protein through all the hoops. As we pulled,
the score would likely vary, and if we placed the hoops
correctly, we could pull the protein back and forth thru
the hoops until we maximized the score along their path. 
See below for more info.

Create hoops (like bands, but the protein can slide through them)

I also made a recipe called shifit0:
This recipe takes the present conformation of the protein
and moves the alpha-carbon (CA) for segment n from its 
present position to the present position of CA for segment
n+1. When done repeatedly for all segments of the protein,
this makes the protein move like a thread along the path
of the protein's alpha-carbons. In a way, the locations
of all the protein's CA's act like hoops for the protein
to slide through.


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, Boehringer Ingelheim, RosettaCommons