I have been working on the Coronavirus puzzles recently, and getting some decent scores, but I have been unclear about where we should be trying to get the protein to bind too.
For example, on Puzzle 4, should all of the protein be wrapping around the the large helix, or can we have some wrapping around too?
As an example, my current solution has one of the editable portions of the protein wrapping around the helix, while the other wraps around the protein and then links up with the group of sheets that have exposed orange sidechains. Is this good, or not within the target?
In round 4, the helix is pre-provided but locked down and is already in the binding groove. Build around the helix to form a stable protein core that can keep it shape while it's floating and waiting to bind with the virus.
It should be noted that rounds 3 and 4 were partially in response to players completely missing the binding site with otherwise good designs in rounds 1 and 2. Check the blog posts and videos up on Foldit's YouTube for more.
First look at coronavirus solutions
https://fold.it/portal/node/2008989
Special update on coronavirus puzzles
https://fold.it/portal/node/2009049
Analysis of protein binder designs
https://fold.it/portal/node/2009115
To make sure, what you are saying is to try to get it all binding near the helix that is not part of the spike protein?
We're still binding the spike protein, and if your design has additional binding contacts to the spike protein, go for it! It's just important to note that if you don't make a stable hydrophobic core (which will usually involve using the helix as one of the walls of said core), you'll lose out on bonus points and (potentially) scientific viability, as proteins without a core might tend to flop about and not take any specific shape most of the time.
