we can make bonds with the ligand
The new scoring method is an improvement, however, it still does not reflect the importance of the protein-sugar bonds.
Example 1: You can score higher with a helix having zero sugar bonds than you can with a loop having five.
Example 2: You can have several loop variations that range anywhere from 3 to 8 bonds but are relatively close in score. Having higher sugar bonding counts doesn't correlate to higher scores--even loop vs. loop.
I still think that the only way to boost the sugar bonding is to award bonus points for each bond. Possibly 25-50 points each?
but to make a protein that can fold like we imagine and that have bonds.
To many score can boost not realistic proteins.
I think the puzzle works well like that, we have to choose the start and save it and if recipes destroy it : reset or reload and redo.
If I recall correctly from the 625 description, this is suppose to help "capture" sugar molecules. If that is the case, the more bonds between the protein and molecule, the better--unless there is some point where an excess number of bonds doesn't make any difference.
If the scoring doesn't take this importance into consideration, we'll end up with few relevant solutions. I understand that the protein itself must conform to the standard rules (clashing, voids, etc.). If all the regular rules are adhered to, a solution with protein-sugar bonds should normally beat a solution with fewer ones. I'm guessing, but I imagine that's why they limited the number of segments that can be added.
Scripts are oblivious to the importance of the bonds because it isn't reflected by the current scoring system. They only way you'd know whether or not you get 6, 10 or 12 bonds would be if the script happened to quit at that point or if you had time to count them while it was running--it has no incentive to remember it.
Because bonds with the sugar are so weak, could it be that hiding the sugar would be better and also boost that score part?
so it is just my perception of the game.
I am not sure the goal is too make the higher number of bonds just to make a stable protein with at least 1 more bond.
I think that the protein have to fold a similar shape with and without the sugar.
In the real world, no super score to bonds with the sugar is allowed.
If the score of the bonds are too high, we will make a sequence that give a different shape in the real life and dont trap the sugar at all and dont make bond at all.
The goal of foldit is not to run scripts to find a good solution, it is to find a good solution and apply recipes to do some of the boring jobs. Design puzzles are one of the last corner of foldit where manual folding is rewarded.