Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 240, at a cost of 55 points per residue. Players may use up to 250 residues in total.
Core Existence (max +2400)
Ensures that at least 35 percent of residues are buried in the core of the monomer unit.
Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.
SS Design (max +500)
Prohibits CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.
Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.
Why does puzzle 1924 score so much lower than prior designable link puzzles? There is no change in the objective bonuses, and there seems to be little change in the designable section.
This is actually a completely different setup from previous puzzles since we are asking you to design a linker between a different set of LCB1-LCB3 termini. It's possible that it is harder to increase your score dramatically in this different configuration. However if you are just talking about the absolute sizes of the score, those are not comparable between puzzles.
I also have the same queries about score. I see some players achieving more than 7000 points. This means that they use better algorithms and may much more processing power than mine. Also I want to ask do you manage Ideal Loops earlier or later in the design because I got some problems with it for this particular puzzle. For example if you know what a-helices and sheet to use prior is easy to fix the ideal loops but if you do not know this makes it harder.
You can achieve these high scores with a clean and stable hand-folded design and the proper optimization-recipes. I use mostly: Cut and wiggle, bandfuze, banded worm pairs, jet or sd multiwalk forever, acid tweaker/tweeker and random idealize. These generally squeeze out enough points provided your design is stable. With stable I mean that it does not form unideal loops when wiggling globally. I try to clean up unideal loops as early as possible. Remix can be used for this or sometimes I have to handfold loops and surrounding segments anew or cut them up and redo. If there is too much torsion or stress in general present on parts of your design it will increase the likelihood that unideal loops will form. So you should take care early that nothing looks too twisted or odd. In terms of the interconnecting cut in the linker between the two binders, I try to put this in a Helix and then use the scheme with bands from n to n+3 and n to n+4 over the cut as it was shown in one of the last newsletters. Then wiggle and the helix will connect nicely with some practice. This only works of course if the helix is correctly pre-aligned and phased (meaning it should look roughly around the cut as if you would cut up an ideal helix). For initial alignment I use Rama map, dragging or bands. Take care that in this step nothing is already overly stressed or skewed. Otherwise adapt your design.
This is my personal opinion which works well for me. Others may have different views, strategies or recommendations. Just experiment with it and find out what fits for you. Happy folding, iwdn
Hi there--thank you for these suggestions! I have also passed the questions from others along to the team.
Thank you for you kind answer. It makes some mentioned subjects more clear to me.