Let certain Design Puzzles input one or more pdb or ir_solution files to make starting structures

Case number:845813-2006295
Topic:Game: Tools
Opened by:jeff101
Opened on:Friday, December 7, 2018 - 14:21
Last modified:Monday, March 11, 2019 - 00:28
I know many have asked for the ability to import pdb files
into Foldit before, but maybe this ability would help more
than it hurts for certain Design Puzzles. I think it would
be interesting to see what we could design by taking parts
of known proteins and loading them into Foldit via one or 
more pdb files. Once the starting structure was loaded in, 
we could mutate its residues to improve its design. 

Similarly, it would be interesting if we could import our
solutions from previous puzzles into a Design Puzzle via
our old ir_solution files. This would let us improve on 
old designs, perhaps making our top scores on each Design 
Puzzle a little higher each time. Loading at least one
ir_solution file from an old evo could make the new design 
count as an evo from the start. 

Perhaps we could combine several pdb and ir_solution files 
to make our starting structure. If multiple files were used, 
Foldit could have the first file give residues 1 to L, the 
2nd file give residues L+1 to M, the 3rd file give residues 
M+1 to N, etc. This would work as long as the final total # 
of residues was in the desired range for the Design Puzzle. 
There could be long blue cut bands between residues L and 
L+1, M and M+1, N and N+1, etc. We would have to find ways 
to shorten these blue cut bands enough that they became 
yellow, at which point we could heal/remove them.
(Fri, 12/07/2018 - 14:21  |  1 comment)

jeff101's picture
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Groups: Go Science

A similar request would be to have more Design Puzzles that let us input solutions from previous Design Puzzles. For example, Dimer or Trimer Puzzles could input their monomers from Monomer Puzzles with the correct number of residues. Also, Monomer Puzzles could input their monomers from Dimer or Trimer Puzzles with the correct number of residues. This seems reasonable because to make a good dimer or trimer complex, it helps to have a stable monomer. If we devote a lot of time in a Monomer Puzzle to making a stable monomer, we don't have to repeat all these steps in a later Dimer or Trimer Puzzle to make a stable complex. We could use more of our time in the Dimer or Trimer Puzzle making the monomers connect in interesting ways.


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