Welcome our new Community Liaison!
To start your week off, we'd like to take a moment to introduce our new Community Liaison, Nova "inkycatz" Barlow. She'll be working on Foldit in addition to other Center for Game Science titles.
A well-established community advocate, Nova's most recent work includes Kodu Game Lab and Project Spark at Microsoft. For those fans of our IRC channel, you may have already spotted her lurking around late last week getting up to speed. She's thrilled to be joining this established community of folders and can't wait to hear your thoughts.
Feel free to say hello and offer your best folding tips!( Posted by inkycatz 81 2386 | Mon, 05/05/2014 - 20:13 | 2 comments )
Predicted Contacts and The Contact Map
It's time to introduce our newly redesigned Contact Map. We've completely redesigned the Contact Map in order to better tackle the contact guided structure modeling targets in the CASP competition. We'll frame these targets as Predicted Contact Puzzles in Foldit.
Our original Contact Map was designed for the legacy "Exploration" Puzzles, and needed to be upgraded badly. With that in mind, we've recreated the Contact Map to deal specifically with the Contact Predictions that we will see in CASP. It should scale better with larger proteins (Veteran users may recall some puzzles where the old map would take up most of the screen). This should let the Contact Map handle any proteins that Foldit itself can handle.
The new Map should be much clearer and easier to use. In addition, it should provide some new functionality that should come in handy during CASP!
First - what is a predicted Contact? A predicted contact is a prediction that two Residues in the protein will be close together, or "in contact". They wont actually be touching (this would be clashing), but will still be fairly close.
Each contact has a "weight" associated with it, which is a measure of the likelihood that the residues involved actually form a Contact in the native protein. The higher the weight, the higher the likelihood. Note that this means some contacts can be incorrect, so a decision has to be made as to which contacts should be pursued.
In Foldit, we are going to try several different approaches to rewarding players for matching predicted contacts. Up until now, we've been re-using the Exploration Puzzle system, which lead to a lot of confusion.
No longer! - The Contact Map is now set up to be independent from the scoring method used to reward matching contacts.
This gives us the ability to run Contact Puzzles in 3 different ways:
* Purely as a visual guide, with no reward for matching contacts.
* In combination with a Filter that will give you a small bonus for matching contacts.
* In combination with puzzle Constraints, which will penalize the score of structures that are missing high-likelihood contacts.
Predicted Contacts are a great domain where players have the potential to succeed where computers have failed, and we've designed the Contact Map to try to give you the best shot at it!
So without further delay, below is a visual guide (You might call it a "map"!) to the Contact Map:
The Contact Map
1. This shows the residues involved in the contact that you are currently hovering over with the mouse.
2. This shows the weight of the contact that you are currently hovering over with the mouse.
3. These black dots show contacts which your current protein model has.
4. This button will clear the selected cells.
5. This button will add a band for each selected cell. The band will be between the two residues involved in the contact, and will have default length and strength. In the future, we plan to set the strength and length based on the contact prediction.
6. The diagonal represents the backbone of the protein. The color of the diagonal indicates the secondary structure for that section of backbone. In this case, it is red, which corresponds to a sheet.
7. An empty color on the diagonal corresponds to a loop.
8. Blue on the diagonal corresponds to a helix.
9. Green cells are predicted contacts. A brighter green means a higher weight, and a more likely contact.
10. The highlighted and outlined regions are the selected cells. When you select a cell, you will see a red or green band on the protein model itself, with color indicating whether you have satisfied that contact or not. You can select a cell by left clicking the cell.
11. Clicking and dragging this bar will allow you to re-size the contact map.
12. The map will highlight the contact you are currently hovering over with a vertical and horizontal bar. Additionally, you will see a yellow band on the protein model itself, which links the two residues involved in this contact.
The Contact Map also allows you to zoom with the mouse wheel. While zoomed in, you can also pan over the map by right clicking the map and dragging.
We've just posted a puzzle which features the Contact Map, which you can find here: http://fold.it/portal/node/997597
We hope you enjoy the new Contact Map, and we're looking forward to seeing how you all use it during CASP!( Posted by jflat06 81 834 | Wed, 04/30/2014 - 20:41 | 5 comments )
Foldit joins the Baker Lab's "War on Ebola"
The Baker Lab is doubling down on its efforts to design a protein that could bind, and eventually treat, the deadly Ebola virus. In the coming months, the lab has plans to design and test thousands of small proteins using recently-developed biochemical techniques. Foldit could play a huge part in this effort, as we have the opportunity to test a large number of Foldit player solutions from Ebola-related design puzzles. Check out Puzzle 879 now to stabilize a helical fragment designed by Baker Lab scientists!( Posted by bkoep 81 1011 | Tue, 04/22/2014 - 02:16 | 0 comments )
CASP11 starts next month!
The CASP organizers have shaken things up a bit for the upcoming CASP11 experiment!
One of the major changes is that for each prediction that we submit, we will be required to provide how confident we are with each residue in the chain.
For example, we might report for our model1 submission of a particular target (with length 181) that residues 1-80 are 100% accurate, but residues 81-85 are 50% accurate and 86-181 are 80% accurate. Then for model2 we might have completely different confidence values: residues 1-20 are 50% accurate, 21-180 are 70% accurate, and we have a confidence of 25% for the last residue, 181.
The organizers have told us that predictions with fewer than 2 different confidence values will be rejected, so this is going to add another layer of complexity to CASP!
The more exciting changes are the new initiatives in CASP11:
Modeling based on predicted contacts,
Modeling based on simulated sparse experimental data,
Structure prediction based on only the correct predicted contacts
The Assisted Structure Prediction Category was first introduced at the last CASP, but unfortunately Foldit was unable to participate in this new category because the puzzle load of the regular CASP10 targets was already too much.
Since this year they are expanding this category to 3 different rounds (up to 4 rounds if they able to include real cross-linking data for certain targets) we want to make sure Foldit is able to participate in these.
Our plan for CASP11 is to post Foldit puzzles for as many of these Assisted Structure Prediction targets as we can, in addition to the targets in the Refinement Category.
For the Template-Based Modeling (TBM) targets, Foldit has never been able to participate in all the TBM targets, but the organizers have added a new initiative for CASP11:
Evaluation of models based on a perfect alignment to the template.
Instead of giving you 3-5 different alignments (that may or may not be correct) in the Alignment Tool like in previous CASPs, the organizers will provide us with the perfect alignment!
Our plan for the TBM targets in CASP11 is to participate in these cases where we can give you the correct alignment.
This just leaves the Free Modeling (FM) category (where there are no templates), which is of course the most difficult category at CASP.
We are happy to announce that the best-performing FM group at CASP10, keasar, will be teaming up with Foldit at CASP11 via WeFold. You can see how well keasar performed at CASP10 in the pdf of the official rankings
The table below shows all the CASP10 groups that submitted at least one model deemed good enough by the CASP10 assessors of the FM category. At the top, with 8 different targets, is keasar followed by everyone else below (including FOLDIT and 2 of the Foldit teams):
What the keasar team is able to do very well is pick out the best server models (denoted by the corresponding green squares: the server models used by keasar for each target that they won) but the keasar team isn’t as good at improving these server models. This is why we are excited about joining forces with keasar by creating a WeFold team where keasar will provide us with their best server picks, and we’ll post those as Foldit puzzles for you to improve even further!
This is our plan for the FM targets.
We also hope to collaborate with other WeFold groups for all the non-FM puzzles that we post, to see if they are able to pick out your predictions better than we can.
In summary, our plan for CASP11 is for Foldit to participate in the Refinement Category, all the new CASP11 categories, and the FM category via WeFold.
Speaking of categories, there will be a new Foldit category for CASP11 (and perhaps a sub-category for puzzles using contacts) http://fold.it/portal/categories( Posted by beta_helix 81 2386 | Fri, 04/04/2014 - 18:20 | 4 comments )
Foldit Science Café in San Diego
Hey everyone! I will be leading a Science Café about Foldit at the Southpaw Social Club, in San Diego, on April 28. The purpose of the event is to engage with the community in a casual, comfortable setting to talk about the exciting science of protein folding and the Foldit computer game. There will be a short presentation on the science behind Foldit, but the event is mostly dedicated to Q & A and open discussion with the audience.
We're very excited about this opportunity to share Foldit in such a personable format! This is also a great chance for any Foldit players in the San Diego area to come together and talk to a member of the Foldit team. Or come share your experience with others who are looking for a way to contribute to cutting-edge scientific research!
The event is free and registration is not required. You can find more information here.bkoep 81 1011 | Wed, 04/02/2014 - 07:58 | 2 comments )