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Exploration Puzzle

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Note: Foldit is no longer offering exploration puzzles. This page is for historical interest only. The "contact map" described here is presented in a different form in contact map puzzles.

Historical description of exploration puzzlesEdit

In exploration puzzles, the objective is to find the most diverse and interesting folds of a protein. You won’t score highly by fine tuning a fold: scoring highly requires you to make drastic changes to the backbone, like swapping sheets or rebuilding loops. You want to find a fold that is different from the folds other people have found. The more different your solution’s fold is, the higher you will score!

So you might ask, “What does it mean for my solution to be ‘different’”?

That’s a good question. There are many ways of measuring how different solutions are. In exploration puzzles, we use something called a contact map.

A contact map is a table which shows you which segments of a protein are making contact. Cells in this table have black squares in them if the corresponding segments are in contact. If two segments are close enough to each other, they make contact. If they are too far apart, they won't make contact.

But how does all of this contact map stuff relate to how different my solution is from others?

Well, each cell also has a background color. Sometimes it's red, sometimes it's white, sometimes it's in-between.

This color isn’t just for looks. If a cell is perfectly red, it means that everyone has a contact there. If a cell is perfectly white, it means no one has a contact there. So to explore, try to get contacts in whiter cells. These will get you the most score, but remember that contacts in red cells aren’t a bad thing either, they just won’t give as many points.<

By exploring and gaining contacts in different areas of the map, you will be awarded Exploration Multiplier. Your normal Foldit score is multiplied by this Exploration Multiplier to give you your ranked score, which is what will show up on leaderboards for exploration puzzles.

ExampleEdit

Ss1

You can bring up the in-game Contact Map by going to Actions > Contact Map or by clicking the panel above your score

Now, that was a lot of reading, and not much doing, so let's give an example for some solid experience.

When you open the puzzle, you will notice the normal score panel at the top of the screen has an extra panel above it. This panel shows your normal Foldit score (Stability) and the exploration multiplier (along with a meter which shows you how close to the maximum multiplier you are). Clicking on this panel will open the Contact Map. You can also open it by going to Actions > Contact Map.

SC

Selected contacts from the Contact Panel show up on the 3D model of the protein.

We can select cells on the contact map by clicking on them with the mouse. This will draw lines between the segments. Red lines mean you don’t have a contact yet, and green means you do. In this case, we don’t have any contacts in these cells.

A basic strategy is to put bands along the contact lines, and then wiggle. this will bring the segments closer and form a sheet.

SD

Placing bands along the contact lines will help bring them closer.

After wiggling, we can see how black squares appeared on the contact map around the region we selected, and the lines on the 3D model turned green. 

You can press clear to clear the selected contacts.

SE

The bands brought the segments close enough to form contacts. You can see the contact lines turned green and the cells on the Contact Map now have black squares in them.

By repeating this process in other areas of the map, you can get more contacts in more places for a greater multiplier. Just remember, your score is based off of both exploration and how good the fold is, so dont forget either component!

Questions and comments on Exploration Puzzles can be found on two 2011 Foldit forum posts: first forum post and second forum post.

More on exploration puzzlesEdit

These puzzles came about because players often tend to drill down on folds which are close to the starting structure. This can be helpful on some puzzles, but on others, we know that the native fold of a protein is actually further away, and so this tendency hurts the chances of finding the native.

In particular, often times we derive the starting structure of a puzzle from its sequence's closest known homolog. In layman's terms, we know how to fold something that is "close" to this protein, so we use an alignment from that fold as our starting structure.

This method also provides us with an estimate of how far away the native is from our starting structure. In most puzzles, the native is a distance away from the starting structure which provides a multiplier of around 2.95.

So basically, if you aren't close to this multiplier, you aren't close to the native. However, being close to this multiplier doesn't mean you are close to the native. The multiplier rewards all exploration equally, so you could have gone the wrong direction and ended up even further from the native than the starting structure.

All this exploration can feel make it feel like you're just exploring out randomly. However in these puzzles, you're actually given MORE information than you're used to (basically, the extra information of how far off the native is). Your direction should be guided by your expertise in knowing which changes are obviously incorrect, and which changes have potential.

Exploring just once and finding something close to the native is near impossible. If some attempt at exploration isn't developing as well as you would like, you should try something different.

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