puzzle picture
Drug Design: C2N transformation
Status: Closed

Summary

Name: Drug Design: C2N transformation
Status: Closed
Created: 11/18/2015
Points: 0
Expired: 11/30/2015 - 23:00
Difficulty: Intermediate
Description: This is the first drug design puzzle! Scientific goal: Can you identify which combinations of atom changes in the binding pocket result in a better binding affinity? Can you do better than medicinal chemists? Change the atoms around and see if you can get a lower score than the posted score. When the puzzle is completely released, we will show which atoms can be designed and compare those to what medicinal chemists did. Feedback goal: What do you think about the drug design tools? Keep in mind, the tools are a simplified version of the full set of tools. Please report if the puzzle crashes and what you did to make it crash. New tools: Ligand Design Tool: The Ligand Design tool allows you to add, delete, and modify atoms in a small molecule. For now, we have only allowed the substitution of carbon (C) to nitrogen (N) and vice versa, but many more of the tool’s features will be unlocked as future puzzles are released. In order to modify a small molecule’s atom, all you have to do is click the “Ligand Design” mode, click on the atom of a small molecule that you want to change, and then click on either “C” or “N” to substitute for that atom. It’s a remarkably simple, but powerful tool to utilize in the drug design puzzles. Ligand View Tool: This tool works by clicking on it and then the ligand. A series of new viewing options will be available. The hydrogen bond acceptor and donor options allow you to view where the acceptor and donor are on the backbone and sidechain. The repulsive grids show you where you will get a bad score if you have atoms in that location. Finally, the ligand isosurface helps outline the binding pocket.
Categories:

Top Groups

RankGroupScorePoints
1Anthropic Dreams10,1050
2Contenders10,0750
3Beta Folders10,0070
4L'Alliance Francophone10,0070
5Gargleblasters9,9520
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Top Soloists

RankPlayerGroupScorePoints
1grogar7 63 15 Anthropic Dreams10,1050
2Bletchley Park 17 35 Contenders10,0750
3viosca 90 1808 Anthropic Dreams10,0240
4bertro 90 101 Beta Folders10,0070
5christioanchauvin 50 20 L'Alliance Francophone10,0070
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Comments

Tue, 11/24/2015 - 06:22
#1
grogar7 63 15
grogar7's picture
User offline. Last seen 3 hours 13 min ago. Offline
Joined: 10/03/2011
Groups: Anthropic Dreams
Wiggle problem

As soon as CI is set below 1.000, wiggle causes protein to explode. This even happens at CI=.999 Makes me think something is wrong :(

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Tue, 11/24/2015 - 16:37
#2
Mike Cassidy 82 43
Mike Cassidy's picture
User offline. Last seen 13 hours 4 min ago. Offline
Joined: 06/24/2008
Groups: Void Crushers
The grids

The acceptor and donor grids vanish sometimes when you are wiggling; you can get them back by moving the slider slightly

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Tue, 11/24/2015 - 19:51
#3
martin.szew 90 1808
martin.szew's picture
User offline. Last seen 22 hours 44 min ago. Offline
Joined: 04/10/2015
Groups: Beta Folders
Wiggle exploding the protein...

It is somehow frustating to press the Wiggle button and sometimes see the protein "explode"... specially for the novice players or anxious players like me...

Probably will be nice to know that local wiggle Works better...

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Tue, 11/24/2015 - 20:18
#4
martin.szew 90 1808
martin.szew's picture
User offline. Last seen 22 hours 44 min ago. Offline
Joined: 04/10/2015
Groups: Beta Folders
From nemo7731 (Thanks)

The problem disappears if you uncheck enable cut bands

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Tue, 11/24/2015 - 20:59
#5
 free_radical 90 1808
free_radical's picture
User offline. Last seen 1 year 35 weeks ago. Offline
Joined: 01/12/2015
Groups: None
Everyone, thank you for all

Everyone, thank you for all the comments and braving this puzzle. I will be following up on the bug reports.

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Wed, 11/25/2015 - 03:39
#6
Skippysk8s 21 30
Skippysk8s's picture
User is online Online
Joined: 06/06/2013
Groups: Gargleblasters
what grids? totally lost

can't find any

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Thu, 11/26/2015 - 18:23
#7
viosca 90 1808
viosca's picture
User offline. Last seen 41 weeks 4 days ago. Offline
Joined: 10/16/2013
Groups: Anthropic Dreams
issues

Global wiggle appears broken. Selected wiggle works.
From the selection interface, cant find the drug design tools.

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Thu, 11/26/2015 - 18:23
#8
viosca 90 1808
viosca's picture
User offline. Last seen 41 weeks 4 days ago. Offline
Joined: 10/16/2013
Groups: Anthropic Dreams
issues

Global wiggle appears broken. Selected wiggle works.
From the selection interface, cant find the drug design tools.

Top
Thu, 11/26/2015 - 19:12
#9
hansvandenhof 90 345
hansvandenhof's picture
User offline. Last seen 3 weeks 17 hours ago. Offline
Joined: 06/04/2012
Groups: Anthropic Dreams
Ligand design tool?

Don't understand how the tools works in relation to scoring. Changing an atom from e.g.N to C gives a significant drop in the score. Score won't go back after changing the atom to its original state.

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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