Predicted Contacts and The Contact Map

Started by jflat06

jflat06 Staff Lv 1

Hey everyone!

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!

Predicted Contacts

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!

drumpeter18yrs9yrs Lv 1

Can we get a range of the weights and how good it is? Like, how good is a weight of .9 per say? I would like to see the same thing that was done with the colors. We were told that wight was bad and dark blue with a black square was "great." Could we get the same thing, but with numbers?

Could we also get a zoom in and out button?

spmm Lv 1

This great jflat, thank you. Especially the accuracy of the cross hairs.
The zoom is fantastic and it picks up the colour differences in the green a bit more when zoomed in.
I am finding it difficult to see the difference in 'weight' easily with the green range, the purply blues seemed much easier to distinguish in the old map, for me anyway.
Being able to actually see the weight numerically means you can still work out which are the better contacts. Just a bit slower.

jeff101 Lv 1

It would be handy to have on the Contact Map or up in the Rank/Score/Conditions box the maximum weight for a contact point in the puzzle's Contact Map and the maximum possible bonus (points from filters) for the puzzle.

Vredeman Lv 1

The new contact works better for me. Good work.
Would a script be able to include the weighting values in its operations?
There are some useful requests regarding visibility.