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1930: Designable Linker Puzzle: Coronavirus Spike Binder
Status: Closed

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neilpg628's picture
User offline. Last seen 1 hour 43 min ago. Offline
Joined: 08/01/2019
Groups: Foldit Staff
Objectives

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 260 residues in total.

Core Existence: LCB1 (max +2400)
Ensures that at least 34 percent of residues are buried in the core of the LCB1-linker unit.

Core Existence: LCB3 (max +2400)
Ensures that at least 34 percent of residues are buried in the core of the LCB3-linker unit.

Core Existence: Linker (max +2400)
Ensures that at least 35 percent of residues are buried in the core of the LCB3-linker 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.

Joined: 08/11/2010
Residue Count actually starts at 230 not 240

Unless you'd like to repeat my instructional waste of a day please start off by adding 10 residues to the alanine linker (e.g. select a segment from the linker in selection interface and click on the "+" choice).

Must. Read. Fine. Print.

Joined: 08/11/2010
clarification

this comment addressed to fellow folders, not the devs/scientists

Joined: 09/24/2012
Groups: Go Science
A video tutorial for this puzzle

Hello, here is a video screen shot of designing a linker using BluePrint for this puzzle.

It took about 42' to get a starting design with all filters ok.

At start, don't look to the score, only look to structure (make parallel helices or sheets), and try first to satisfy all bonus.

When your conditions are all met, you can start with recipes, always verifying that the filters are still ok (if not, start again with another recipe).

Suggested recipes after this first design: Quickfix (not allowing any filter loss > 5-6 pts) or JET

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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