Centroid Mode

It’s time to work on some larger proteins.

We’ve just posted a new puzzle with 398 residues. This protein is too large for the normal Foldit client to handle. Because of this, we've introduced “centroid mode”. Where normal “full atom mode” puzzles have to calculate the score based on individual atom positions of all the sidechains, “centroid mode” uses approximations to speed up the process.

This new method of scoring is a radical change compared to the normal “full atom mode” score function. Tools such shake, mutate, and wiggle sidechains have been disabled because the data required to run them is not longer being generated. Other tools such as wiggle and clashing importance are ostensibly the same, but under the hood they are working in a very different way. You will find these differences require your Foldit strategies to change. We encourage you to try out new methods of working with the protein that take advantage of these differences.

One of the most apparent changes will be in how clashing importance works. In “full atom mode” when you turn the clashing importance down, there are many other elements of the score that normally take over and generally compress the protein. In “centroid mode” these scoring elements do not exist to the same extent. Because of this, you will see that the clashing importance slider does not perform exactly as it did before.

We would appreciate your input on these changes, and want to work with you to improve this new method of folding proteins. This is the first step towards Foldit players being able to tackle entirely new sets of problems that were untenable before.

( Posted by tamirh 79 2078  |  Mon, 04/29/2013 - 22:48  |  3 comments )
Joined: 12/06/2008
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Send this concept back to the Abyss from whence it came.

Part of the idea of folding a protein into the "best" shape was to place sidechains in optimal positions: to better allow compression the thing and to allow secondary structures to align more favorably.

Centroid mode hamstrings us. There is no such thing as an approximate sidechain. This will make it harder, not easier to us to find native structures.

jflat06's picture
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We agree that 'part' of the best shape includes the sidechain positions, and that's why full-atom (normal) mode exists.

However, you'll find the Baker lab scientists disagree with the statement that "There is no such thing as an approximate sidechain."

Centroid mode is commonly used by the Baker lab in prediction during the initial stages to find reasonable backbone conformations before moving on to refining the sidechains. The main benefit, of course, is speed. Centroid mode lets us run faster puzzles, and larger puzzles. Size is something that has been preventing us from running a lot of real-world application puzzles, which was part of the motivation for centroid mode.

"This will make it harder, not easier to us to find native structures."

- Certainly this will be true initially. You've had years to practice with full-atom mode, and only a small amount of experience folding at this different level. Centroid mode will require developing a new skill set, and a new way of looking at things.

Joined: 11/16/2012
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the puzzel

i find this puzzel extremly hard, but that's why i love it and i love the idea that fold it is expanding to larger puzzels. keep them coming! :)

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