Tournament Phase Two puzzles reposted!

Started by bkoep

Bruno Kestemont Lv 1

It seems that scripts with "Are conditions met" option don't act as expected.

Is it a bug ? or should we adapt most recipes with a specific filter condition ? ;P

jeff101 Lv 1 

If you included an RMSD-dependent bonus,
I think it would also act like a shield, 
keeping recipes from exploring the range 
where RMSD < 2.5 Angstroms (I call this
range the "RMSD 0 basin" below).

Say you started a puzzle with the protein 
chain linear & fully extended. Odds are 
this would have RMSD > 2.5, but the overall 
score would be very low. Using wiggle or 
just about any recipe, the score would 
gradually rise, and the RMSD would likely 
change. If the designed structure with 
RMSD = 0 has a large basin of attraction 
or large funnel in the energy landscape, 
many folding pathways will eventually 
fall into this basin or funnel. Thus, 
as your score rises, the RMSD value will 
gradually decrease and might drop below 
2.5. When the RMSD drops below 2.5, one 
could say the structure has fallen into 
the RMSD 0 basin.

With no RMSD-dependent bonus, there is 
no penalty to recipes for continuing 
deeper into the RMSD 0 basin. A player 
must notice what has happened ("my score 
has a red line through it and I am no 
longer getting credit for it!") and 
take manual corrective actions.

With an RMSD-dependent bonus, structures 
falling into the RMSD 0 basin will face 
a drop in score, and this drop may be 
enough to redirect recipes away from 
the RMSD 0 basin.

bkoep Staff Lv 1

You should aim to get the highest score you can. The higher your score, the more you hurt the partition function of the design. It doesn't matter so much whether you pass the score of the starting pose. For most of these puzzles, we don't expect anyone to pass the starting score.

If you do manage to pass the score of the starting pose, that means you have found a decoy that is more stable than the starting pose. This would be really bad news for the design, and that design would not definitely not win the tournament (and in that case I would recommend you turn your attention to another partition puzzle). But that doesn't necessarily mean you "win" the partition puzzle. After all, someone else could find another decoy in the same puzzle that scores even better.

jeff101 Lv 1 

A long-tailed form for the 
RMSD-dependent bonus could be:

bonus=1000/(1+(2.5/RMSD))

which gives the bonuses below:

RMSD    bonus
-------------
 0          0
 0.3125   111
 0.625    200
 0.8333   250
-------------
 1.25     333
 1.6667   400
 2.5      500
 3.75     600
 5        667
-------------
 7.5      750
10        800
20        889
huge     1000

As you can see, this bonus rises fast for 
RMSD<2.5 and more slowly for RMSD>2.5. 
The long-tail at large RMSD will encourage 
recipes to explore increasingly larger RMSD 
values, even after the RMSD has passed 2.5.

Bruno Kestemont Lv 1

Can you answer the question by susume here:
https://fold.it/portal/node/2005660#comment-37539

According to what susume observed, if any player reaches about 30 pts from the stating pose, it'd be enough to say that the puzzle isn't very stable. This would be a signal to other players to forget this puzzle and to try contesting other puzzles. Alternatively, it can be interesting for science to try another pose for the same puzzle (in order to fulfill other slices of its partition function).

Sorry for the dude questions and thanks for your patience.

alcor29 Lv 1

If we can't get within 100 energy points of the original given that
[E=(F-8000)/-10], then is there a benefit? If we can't get within 50 energy points?