puzzle picture
708: Multi-Start 76 Residue Symmetric Dimer
Status: Closed

Summary

Name: 708: Multi-Start 76 Residue Symmetric Dimer
Status: Closed
Created: 05/02/2013
Points: 100
Expired: 05/10/2013 - 16:00
Difficulty: Advanced
Description: We are giving you a 76 residue symmetric dimer to design. This is a multi-start puzzle, with three starting points that you will cycle through when you reset the puzzle. There are two filters enabled on this puzzle. The ResidueIE filter ensures PHY, TYR, and TRP residues are scoring well. The "Core Exists" filter ensures the number of residues in the core is at least 30%. We hope these filters will help you design proteins that the scientists will be able to create in the lab. Thanks to Steven Pletsch for providing the solution from Puzzle 676 that is being used for the starting structure for this puzzle. This is just a starting point, you are free to redesign the entire protein in this puzzle.
Categories: Design, Overall, Symmetry

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Comments

tamirh's picture
User offline. Last seen 6 years 18 weeks ago. Offline
Joined: 05/11/2012
More Info

We are continuing to work on getting rid of the filters, but at this time we still need to enable the "Core Exists" and "ResidueIE" filters. We are working with the scientists in the Bakerlab to come up with new ways to achieve the same results without the filters, but we ask for you to bear with us until that happens.

These filters are nowhere as slow as the 'Layer Design' filter, so hopefully they do not hinder your puzzle progress and enjoyment of design.

One reason we were able to remove the 'Layer Design' filter is because we are now using a score term called 'envsmooth'. What this term does is look at the environment around each amino acid and determine if it is statistically similar to the environment found in similar amino acids in native proteins. In earlier design puzzles, this score term was not used. Initially when we used this score term players were able to get high scoring crazy solutions in devprev. We have modified it so that should no longer be possible.

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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