puzzle picture
1653: Y1 Receptor virtual screening
Status: Closed


Name: 1653: Y1 Receptor virtual screening
Status: Closed
Created: 03/25/2019
Points: 100
Expired: 04/02/2019 - 23:00
Difficulty: Advanced
Description: THIS IS A MULTISTART PUZZLE - Click "RESET PUZZLE" to cycle through each of six starting structures.

One computational approach frequently used in drug discovery is "virtual screening". In this technique computational methods are used to look at a number of different small molecules and predict how well each binds to the protein. By testing the small molecules computationally, you can avoid the cost and hassle of making and testing those compounds that aren't predicted to bind the protein well.

In this example, we have a number of small molecules which bind to the Y1 receptor with different affinities. We're curious if the top scores that Foldit players can find for each molecule correlate with the ability of the small molecule to bind to the receptor. For this puzzle we have six different small molecule compounds placed in the binding site of the same protein structure, with each compound as a different multistart. Try to find the best scoring docked conformation of each of the six small molecules, and the best scoring docked conformation (best small molecule) overall.

As a ligand docking puzzle, focus on finding the best position and interactions for the ligand (the residue in the middle of the alpha helices), rather than changing the protein. It's important that you try each of the six ligands, as the ligand you start with isn't necessarily the best scoring ligand. Use the "Reset Puzzle" tool to restart the puzzle with a different ligand. Remember that you can use the "Save Solution" and "Open Solution" tools to save and go back to a particular structure/small molecule.

This is a follow on of puzzles 1441, 1446, and 1503.

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Joined: 06/24/2008
Groups: Void Crushers

It is not working.

frood66's picture
User offline. Last seen 8 hours 55 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
this is outstanding! how many

this is outstanding! how many puzzles will be affected by this?

Please let us know - then we can come back later. :)

jeff101's picture
User offline. Last seen 2 hours 23 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Scores for each starting structure:
       overall     ligand / residue 290        
        Foldit     overall      bonding
#        score       score     subscore
1   -16783.163    -13040.9     12.8
2     6715.416     -1304.1      0   
3    -6313.439     -7807.1      0   
4     5291.097     -1999.3      6.6 
5    -2088.165     -5693.3      7.2 
6   -11255.732    -10308.1      2.5 
frood66's picture
User offline. Last seen 8 hours 55 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
I have to say

this is (by admission from FC) a true lab rat puzzle.

I suggest it plays no part in overall scores/ranking

FC - please set this one aside

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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