Contact map tool - Exploratory score useful outside of exploratory puzzles (use in Structure Prediction recipes)

Case number:845813-989551
Topic:Game: Tools
Opened by:Seagat2011
Opened on:Tuesday, April 12, 2011 - 09:34
Last modified:Monday, October 6, 2014 - 21:56

The exploratory score in the contact map tool may be useful to detect, analyze and visualize residue co-locations in protein and mixed polymer structures outside of traditional exploratory puzzles. A recipe writer could: a. select an atom along the polymer chain; b. chooses an atom that is commonly present in every residue of the nucleic acid and/or protein structure. c. defines a distance from these atoms 1fu (foldit unit) (3-15 A). The contact map could detect every residue that is located within the defined distances from the defined "backbone" atom(s), following the player manipulating the protein in 3-D space, creating new associations for analysis in the solution space; the writer could then create an internal table-like visualization (Residue Contact Map), with an attendant exploratory score, and calculate the highest scoring frequency of every possible residue pair (Residue Contact Table) in the observed structure. The recipe writer could then restore the structures with the highest score.

(Tue, 04/12/2011 - 09:34  |  4 comments)

Joined: 08/24/2010

correction: The recipe writer could restore the highest scoring conformation, according to criteria pre-set in our recipes, and then set structures accordingly.

Joined: 06/17/2010

Wow, great idea. Voted up :)

jflat06's picture
User offline. Last seen 3 days 23 hours ago. Offline
Joined: 09/29/2010
Groups: Window Group
Status: Open » Open

This is something I've considered and would like to do (in some form). It probably wouldn't be hard to just make the Contact Map available in normal puzzles. I'll consider adding this in when I have more time (hopefully with some better script hooks).

Joined: 08/24/2010
Status: Open » Open

How is this feature progressing?


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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