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Since CASP is monopolizing the available puzzle spots, we'll be posting some non-CASP puzzles to try out (available in the Foldit Developer Preview, see below) in case you want a change of scenery (or a preview of what is to come).

The first such puzzle has just been posted, it's called "Flu Puzzle Testing" and will probably be the first non-CASP puzzle to be released once we have an opening in the puzzle queue.

These puzzles will not be scored and your solutions will not be analyzed.
I will add to this post anytime a new puzzle is added.

_________________________________________________

Q: How do I try out the Foldit Developer Preview?
A: Locate your Foldit data directory (see next question). Open the file options.txt and change the update_group variable from "main" to "devprev".

Q: Where can I find the Foldit data files?
A: The data files are in different places depending on your OS:

on Windows:
if you installed after 8/23/2011, they will be in your installation directory (the default is C:\Program Files\Foldit\ or C:\Program Files (x86)\Foldit\)
if you installed prior to 8/23/2011:
on Windows XP at C:\Documents and Settings\All Users\Application Data\Foldit\
on Windows 7 and Vista at C:\ProgramData\Foldit\
on a Mac, Ctrl-click on the app and choose "Show Package Contents, then go to Contents/Resources
on Linux, is is the Foldit directory

Q: I've had enough of the preview! How do I go back?
A: In your options.txt file (see first question), just change your update_group variable back to "main" from "devprev".

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I added a different version of the Flu Puzzle Testing puzzle

Flu Puzzle Testing 2

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I added a new puzzle:

Tissue Regeneration Puzzle

A different version of it will hopefully be posted soon (for everyone who is getting a bit sick of CASP puzzles).

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I added a different version of the Flu Puzzle Testing puzzle

Flu Puzzle Testing 3

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I added yet a different version of the Flu Puzzle Testing puzzle

Flu Puzzle Testing 4

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I've posted an experimental symmetry puzzle.

We've run this puzzle before.

Previously, the two locked regions were cut apart from rest of the protein and secured with constraints. This was because we want to keep this region essentially the same.

I've added functionality to let us place constraints across the symmetric interface. Now, instead of using cuts, we've just locked both regions, and put strong constraints securing the two locked regions together in that conformation.

It should now be technically possible to move them, but it should be very hard, and score poorly. If you're able to modify the relative position of the two locked regions significantly, and still score well, this is a problem, and we'll want to know about it.

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Trying to get rid of scoring artifacts in design puzzles

We have reposted Puzzle 571: Tissue Regeneration Design Puzzle, this time with a new patch designed to help with scoring artifacts.
The Puzzle is in devprev and called: residueIE filter test

Many players had pointed out that saturating the helix with aromatics was leading to high scores, but unrealistic structures:
http://fold.it/portal/node/992879#comment-18149
&
http://fold.it/portal/node/992544
&
http://fold.it/portal/node/992899

We have added a patch to the identical puzzle in hope that this will help with the problem.

Please let us know your thoughts, thank you for your help and patience with this!

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Feel free to leave any feedback about the above puzzle

in the puzzle comments: http://fold.it/portal/node/993382

Thank you.

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what is an "aromatic" ?

what is an "aromatic" ?

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What are aromatics?

http://en.wikipedia.org/wiki/Aromatic_amino_acids says the aromatic amino acids are phenylalanine, tryptophan, histidine, and tyrosine.

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I'm not sure the game has

I'm not sure the game has smell-o-vision so we can tell if an amino acid is aromatic...

Joined: 08/29/2010
Its just the category of

Its just the category of amino acids used to get the scoring artifact bug there... nothing that you have to smell...

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tennis rackets

The aromatics are the sidechains with rings on stems - some people call them the "tennis rackets."

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Trying AGAIN to get rid of scoring artifacts in design puzzles

We have reposted Puzzle 571: Tissue Regeneration Design Puzzle, this time with a newer patch designed to help with scoring artifacts.
The Puzzle is in devprev and called: residueIE filter test

This is the same puzzle as before so you can hopefully notice that your score will be lower for bad-looking structures.

Many players had pointed out that saturating the helix with aromatics was leading to high scores, but unrealistic structures:
http://fold.it/portal/node/992879#comment-18149
&
http://fold.it/portal/node/992544
&
http://fold.it/portal/node/992899

We have added a patch to the identical puzzle in hope that this will help with the problem.

Please let us know your thoughts, thank you for your help and patience with this!

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as was pointed out in the comments of the News Post

The scores were not reset since this puzzle will not be scored, so it doesn't matter what the scoreboard reads.

We wanted you to be able to load in ALL your previously high-scoring solutions that had poor designs, so that you could tell if our fix works and indeed they don't score as well as before.

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I have reposted the above puzzle as a separate puzzle:

PLEASE MAKE SURE YOU HAVE THE LATEST DEVPREV UPDATE WHEN TESTING THIS PUZZLE, thanks!

http://fold.it/portal/node/993485#comment-19756

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Since so many things went wrong with the Sepsis Puzzle...

we want to post the newest version of the Sepsis Puzzle in devprev first, to make sure we've properly fixed the bugs!

Please try it out and post your thoughts in the puzzle comments: http://fold.it/portal/node/993550

Thank you again for your patience and your help debugging this one.

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BETA: Symmetric Hub Test

I've just posted a puzzle to devprev. The puzzle is set up as a tetramer that's rooted to a hub. Feel free to try it out and let us know if you find any issues!

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Please give us your feedback on this Symmetric Hub puzzle

in the comments for that puzzle: http://fold.it/portal/node/993658

Also, we want to repost a similar puzzle to 633... but want to make sure that the latest fix in devprev has solved the previous memory issues for Windows users.
If you had those issues with Puzzle 633, please test it out again with the new devprev client and let us know if that nasty bug has been fixed: http://fold.it/portal/node/993596#comment-20017

Thank you for your help! The last thing we want is to push the devprev update to main and post a new puzzle that still has the exact same issues!

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Hopefully the final test of the residueIE filter

I just posted a new puzzle in devprev to make sure all the memory leak issues with the residueIE filter are taken care of.

It's called: ResidueIE Filter Final Test

Please leave any feedback about it here:
http://fold.it/portal/node/993669

Please make sure you are using the latest devprev client and thank you for testing these puzzles!

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New Puzzle - Test Symmetry Puzzle

This puzzle uses some symmetric scoring options which we have not used before. Try it out and see if there's anything odd about the behavior of the game's tools.

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this puzzle has no mutable sidechains

Can you post a mutable one for complete testing?

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New Puzzle - Test Symmetry Layer Puzzle

This puzzle uses a new feature called Layer Design. It will restrict what residues can mutate to based on its position in the protein. Please try it out and see if you find anything odd about it. Thanks!

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New Puzzle - BETA Dimer Hub Test

What we'd like to test with this puzzle is whether anyone is able to move the locked segment that is right next to the hub. It should not be able to move, and if it does, it's a bug. Please let us know if you manage to do it!

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New Puzzle - BETA: Symmetry with LayerScore Filter Test

http://fold.it/portal/node/994303

This puzzle features a new filter that we have been working on that should help iron out some of the issues we've been seeing with design puzzles. The filter will identify two main regions (the core and the surface) of the protein. In this puzzle, you are required to have 30% of your residues inside the core of the structure. What this means is that you should not be able to make structures that have no 'inner' region.

What we'd like to test with this puzzle is whether the filter correctly identifies your protein core and if the filter makes sense while you are doing your folding. Proceed with the puzzle as you would fold a symmetric design puzzle. Let us know any comments or bugs you have on it.

Thanks

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New Puzzle: TEST Dimer Hub

This is a semi-repost of an earlier beta puzzle that had issues:

What we'd like to test with this puzzle is whether anyone is able to move the locked segment that is right next to the hub. It should not be able to move, and if it does, it's a bug. Please let us know if you manage to do it!

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We're bringing the Sepsis Puzzle back!

But we want to make sure it doesn't have as many issues at the first time we posted it (http://fold.it/portal/node/993431).

Please help us by testing the new puzzle out in devprev, "Sepsis Testing": http://fold.it/portal/node/994570

Please report any bugs in the puzzle comments or feel free to open up a new feedback about it.

Thank you very much for beta-testing, as we much rather catch these issues before these design puzzles are posted!

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New Puzzle: BETA Catalyst Hbond Test

This is another iteration of the Dimer Hub. This time, we've added a bonus for forming an Hbond to an atom on the hub.

What we'd like tested is the Hbond bonus - make sure you get the bonus if and only if you have at least one hbond to the highlighted atom (you can highlight the atom with 'show').

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New puzzles: BETA 60res trimer design test

These puzzles are testing weights for the envsmooth (smoothed environment) score term.

What this term does is look at the environment around each amino acid and determine if it is statistically similar to the environment found in similar amino acids in native proteins. In earlier design puzzles, this score term was not used. In puzzle 695 we added this score term and weighted it very highly (at 3.0). We are now testing out smaller values for this score term. Ideally we want to use the highest value for the term possible that does not interrupt your play styles and enjoyment. Please test out the differences you see with shake/wiggle/mutate/running your scripts and using your general techniques you've created for symmetric design puzzles.

You will be able to load in your solutions from 695, and also load back/forth between the 4 different devprev puzzles that are testing envsmooth.

One other thing to keep in mind is how puzzle http://fold.it/portal/node/994886 reacts differently also. There are more variables that are changed in this version, not just envsmooth.

Thanks for all the help!

List of puzzles:
http://fold.it/portal/node/994883
http://fold.it/portal/node/994884
http://fold.it/portal/node/994885
http://fold.it/portal/node/994886

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New Puzzle: Centroid Test

This is a test for a new puzzle option - centroid mode. In centroid mode, sidchains are represented as a single large atom. This means no shaking since there's only one position. It also means the puzzle should be quite a bit faster, letting us run larger puzzles.

We're interested in testing for bugs, as well as thoughts on performance. Your feedback would be appreciated!

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The above puzzle has been delayed...

We'll keep you posted when it comes back!

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New puzzle: BETA 60res trimer

This is another 60residue trimer test. There have been fixes in the score function and we want you to test the puzzle out. See comment #28 for more details about what has changed.

The new test puzzle is here.

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Please BETA-TEST: Flu Puzzle Core Redesign with Conditions

I just posted a new Flu Puzzle in devprev.

We'd like you to test out this upcoming puzzle, because it uses an RMSD Condition and we haven't posted a puzzle with RMSD conditions in a while.

Please try to Redesign the Core of this Flu Design Puzzle, without moving the protein more than 2 Angstroms from the starting conformation.

Let us know of any issues with the conditions. You can open a feedback or post it in the puzzle comments:
http://fold.it/portal/node/995159

We'll have a Scientist Chat in the coming week specifically about this puzzle, once we ensure that it's bug-free and ready to go!

Thanks again to all our beta-testers!

If you want to help us out, but have never used devprev, please read the section:
"How do I try out the Foldit Developer Preview?" in the FAQ: http://fold.it/portal/info/faq

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New puzzles: BETA 76res symmetry design test

These two puzzles are variations on the last design puzzle. We've made slight changes to how the new envsmooth score term behaves (see tamirh's comment about envsmooth above). We'd like you to try these two puzzles and let us know how both of them play, and if either of them behaves preferably to the other. This change is targeted specifically toward the packing of the protein core, so try to explore the core residues.

Please let us know of any bugs or performance issues, and thanks for helping us improve Foldit!

The new puzzles are here and here.

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NEW PUZZLE:

BETA: does this ED puzzle crash your computer?

Before we post the next Electron Density Puzzle, we want to make sure it doesn't crash your computers (particularly Windows machines). Please let us know if this puzzle causes your computer to crash.
Don't spend too much time playing it, we really just want to make sure it loads and runs ok... since it works fine on all of our machines.

Please report any problems here:
http://fold.it/portal/node/995257

Thank you!

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New Puzzle: BETA 725 Wiggle Debugging

It's become clear that the the "broken wiggle" in recent design puzzles is not just one bug, but several—some of which have may have been lurking in the shadows for some time. Since it seems to be a complex issue, we want to make sure that the wiggle problems we reproduce here reflect the same problems you have been reporting in your feedback; there seem to be conflicting opinions about how the filters are affecting wiggle. Please try out a few wiggle moves that have been giving you trouble in puzzle 725, and let us know if this puzzle behaves any differently.

You can post your comments here: http://fold.it/portal/node/995292 . And don't forget you can send us solutions with the Upload for Scientists button!

Thanks!

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New Puzzle: BETA 725 Wiggle Debugging Round 2

We're homing in on a couple possible sources of this "sticky wiggle" problem from puzzles 720, 721, and 725. Please try out the new devprev puzzle (a modified repost of puzzle 725), and let us know if wiggle behaves differently from Puzzle 725. Since the original puzzle has already closed, we've posted a replica of Puzzle 725 here, which you can use as a reference for known "sticky wiggle" behavior.

You can post your comments here: http://fold.it/portal/node/995325 , and thanks for your help! Your continued feedback has been immensely helpful in diagnosing this problem.

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New Puzzle: BETA Tetramer Design with Wiggle Fix

The new devprev release contains changes that should help some of the "sticky wiggle" problems from puzzles 720, 721, and 725. Try out this new devprev puzzle and tell us what you think! Look out for "sticky wiggle" cases (any instances where wiggle freezes unexpectedly and needs to be manually restarted) and make sure that all of your recipes are working.

You can post your comments on the puzzle's webpage here: http://fold.it/portal/node/995414 . We appreciate your feedback!

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Please try out this symmetry design puzzle repost

Please try out this Repost of Puzzle 742: 65 Residue Trimer: http://fold.it/portal/node/995587
We hope the latest update to devprev (http://fold.it/portal/node/995568) has fixed the sticky wiggle bug once and for all!
Please post feedback about this puzzle in the puzzle comments: http://fold.it/portal/node/995587

Thank you!

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New puzzle: BETA Predicted Contacts

This new puzzle type looks a lot like an exploration puzzle, but it has a different goal. Instead of trying to avoid residue contacts made by other players, we're giving you a set of residue contacts that can boost your score. Bring up the Contact Map (Main menu in Selection mode, Actions tab in Classic) to see which residue pairs are predicted to make a contact. Bringing these pairs of residues close together will increase your 'Contact Multiplier'. Try out this puzzle and tell us what you think!

All feedback is welcome in the puzzle comments: http://fold.it/portal/node/995922

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BETA 300 Residue Centroid Test + BETA 300 Residue Full-atom Test

We've just re-posted the 300 residue protein to devprev after making some fixes/changes to centroid.

We've also provided a Full-atom version of this 300-res protein for the sake of comparison.

Let us know if you see any bugs, and what performance differences you notice!

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Fragment Filter + Remix

This is a player solution that has several bad fragments. You should be able to see the bad fragments by clicking 'show' on the filter.

The Remix tool should be available, so try and use it on the bad fragment regions to resolve them.

Any feedback on both the Fragment Filter and Remix Tool is appreciated!

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Remix with Symmetry

This puzzle may help us figure out why so many players experienced crashes on Puzzle 814.

This is a repost of an old C2-symmetry puzzle with the new Fragment Filter and Remix Tool. Try it out with the scripts and tools that crashed Puzzle 814 and let us know how it fares!

Your feedback is welcome in the puzzle comments: http://fold.it/portal/node/996469

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Saving and loading with symmetry

In response to this feedback topic, the latest devprev update includes a fix to "circumvent" the loading problem many people were seeing in the latest symmetric puzzle. Unfortunately, we're still unsure of the root cause of this bug, so we're continuing to gather information on the problem.

There's a new Broken Symmetry Loads puzzle in devprev. Please try it out, run some of the scripts you might have run on the interface redesign puzzles, save your solutions regularly and try loading them back into the client. Let us know if you continue to see the saving and loading problems you previously experienced. Your help is much appreciated!

You can post your comments on the puzzle page here: http://fold.it/portal/node/997310

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New type of contact map puzzle in devprev!

We've introduced a new type of constraint in this puzzle that is more appropriate for the information in predicted contacts. Satisfied contacts contribute directly to your score and are compatible with wiggle and shake, but there is no penalty for unsatisfied contacts. We're excited to introduce this before the first predicted contacts targets of CASP11, so try it out and leave your feedback in the puzzle comments here:
http://fold.it/portal/node/997776

Thanks to all of our devprev players for helping us improve Foldit!

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New design filter in devprev!

We've developed a new Secondary Structure filter, which measures the number of residues in helices or sheets. Rather than depending on the player-assigned secondary structure, the filter uses a DSSP algorithm to determine secondary structure based on hydrogen bonding patterns. As many of you know, Foldit naturally favors helices over other types of secondary structure, so the top-scoring Foldit designs are invariably helical bundles. This filter can limit the amount of helices in top-scoring designs, and we hope it will encourage players to explore new and different folds without having to compete with simple helical designs!

Try out the Secondary Structure Filter in the latest devprev puzzle, and leave your feedback in the puzzle comments here:
http://fold.it/portal/node/998126

Thank you!

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New electron density puzzle in devprev!

Now that CASP is over, we'd like to start posting electron density puzzles again. There were some behind-the-scenes changes with the New Chapter update earlier this year, but we think electron density is ready to go! Try out this puzzle and let us know how it plays!

Please leave your feedback in the puzzle comments here:
http://fold.it/portal/node/1998642

Thank you!

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New Debugging Hydrogen Bond Network Puzzle

Hi everyone, we've reposted Puzzle 1087 here for debugging purposes. We've made some changes recently so that Foldit can report a lot more debugging information with players' solutions. See if you can reproduce the scoring issues that players were having when loading in solutions, and let us know when you do! Your help in this is much appreciated!

Check out the puzzle here:
http://fold.it/portal/node/2000825

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Electron density puzzle in devprev!

Please check out our latest devprev puzzle! It is a clone of a previous puzzle, and we just want to make sure that recent changes to the game have not affected the way Foldit displays electron density. Open up this puzzle and make sure you can interact with the density as you normally do! Please leave your feedback in the puzzle comments:

http://fold.it/portal/node/2001319

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New puzzle in devprev!

Please check out our new design puzzle in devprev. The puzzle includes two new features: a filter that grants players the ability to temporarily add "extra" residues; and a new Rama Map tool that gives players better control over individual residues. Please try out these features and let us know of any problems. Your feedback is much appreciated!

Please leave feedback in the puzzle comments:
http://fold.it/portal/node/2002161

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New devprev puzzle with Ideal Loops Filter!

Check out the new devprev puzzle, which debuts a brand new filter! The Ideal Loops Filter is meant to encourage the use of the Ideal Loops that are displayed in the Rama Map.

Try loading in your solutions from Puzzle 1242, and let us know what you think! Please leave your comments on the puzzle web page:
http://fold.it/portal/node/2002515

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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