Secondary structure tool

Case number:845813-992595
Topic:Game: Tools
Opened by:mbinfield
Opened on:Saturday, May 5, 2012 - 14:27
Last modified:Tuesday, May 8, 2012 - 10:34

It's too difficult to manually create secondary structures, especially helices. By this I mean creating the actual shape, not assigning the shape in structure mode. I'm told by better players that a helical structure can be created easily enough by banding the correct segments and using the rebuild tool, but that's tedious and I can rarely get it to work. We need a simple tool to automatically rebuild a portion of the protein into a specified secondary structure.

This would be similar to partial alignment, except that foldit would thread to an idealized secondary structure rather than to a real model protein. Basically we should be able to hit a button for "helix", enter a start and end segment, and have a helix created between those segments (probably creating a cut-point in the process.) Even for veteran players who are good at manual folding, I suspect this would be a time-saver, and for those of us who are not so experienced, it would be a huge help, especially in design puzzles. Difficulty in making the secondary structures I want is a major barrier to creativity; I often abandon an idea because I'm incapable of implementing it or because it would take forever to get what I want. If I could create the secondary structures instantly, I'd have much more time and energy for actual design.

I'd mostly use this tool for beta-helices, but if the capability were implemented, it would be nice to also have options like straight sheet, beta turn, or pi-helix.

(Sat, 05/05/2012 - 14:27  |  6 comments)

infjamc's picture
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You can write a helix-forming script by asking the program to add bands to the needed locations. But the tricky part is that such scripts can often end up deforming the rest of the protein. It would be nice if there were a way to manually insert cut-points so that one could turn a selected section into an idealized helix/sheet and then glue the protein back together...

Joined: 06/17/2010

Hmmm looks like my "idealize button" idea is coming back :D

brow42's picture
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What I didn't realize until recently is that the rebuild tool takes the SS assignment into consideration. It will take forever if you only have it set to loops (which have no preferred twist) but much faster if you rebuild it as a helix (which go 180-65-65ish). So if you set it to helix, and make sure the end points aren't too far apart (because the helix is shorter) the rebuild tool will eventually turn the SS helix section into a helix. You can also see if the scripts you are running have an option not to turn everything into a loop. Scissors tool combined with rebuild will make making helices almost trivial.

It does the same thing for making straight sheets, but only if you have the SS set to sheet.

Joined: 06/17/2010

All 4 thumbs up for scissors tool!

Joined: 08/24/2011
Groups: Go Science

I didn't realize either that the rebuild tool takes structure assignment into account. I discovered that yesterday. That makes the case for my suggestion weaker, but I'd still love to have a tool that immediately makes a perfect beta turn or straight sheet, and I still think that it would be useful to have a helix creator that didn't require multiple steps.

spmm's picture
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Joined: 08/05/2010
Groups: Void Crushers

oh dear - not all helixes are perfectly straight, nor are all sheets perfectly flat - I suspect that what we are seeing and feeling is the loss of the manual rebuild.


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