puzzle picture
2043: CD47 Binder Design: Round 1
Status: Closed

Summary

Name: 2043: CD47 Binder Design: Round 1
Status: Closed
Created: 09/10/2021
Points: 100
Expired: 09/17/2021 - 23:00
Difficulty: Intermediate
Description: Design a protein that can bind to CD47! This puzzle enables AlphaFold predictions for your designed binder. Once you've designed a binder for the target, upload your solution for AlphaFold using the AlphaFold prediction tool. AlphaFold will predict the structure of your binder chain only (i.e. in the unbound state, in the absence of the target). If you load this prediction, then Foldit will attempt to align the prediction with your solution (i.e. in the bound state, making an interface with the target). If you continue working off of the AlphaFold prediction, you may need to make adjustments at the interface where the binder interacts with the target.

CD47 is a protein displayed on surface of human cells. Normally, CD47 is presented to the immune system as a "friendly" signal, and can prevent an over-zealous immune system from attacking healthy human tissue. However, some types of cancer will over-produce CD47 as a way to evade the immune system, camouflaging a tumor as "friendly" human tissue. A protein that binds to CD47 might be useful for treating these types of cancer. We'd like to design a protein binder that can block CD47 recognition by the immune system, and allow immune cells to attack tumors in the body.

In this puzzle, we've presented a section of the CD47 target that is recognized by the immune system. The backbone and most of the sidechains are frozen, except at the binding site, where flexible sidechains are shown in color. Players can design a new protein that can bind to these sidechains and block CD47 recognition. In order to bind the target, designs will need to make lots of hydrophobic contacts and satisfy any polar atoms that are buried at the interface. But designs will also need to have lots of secondary structure (helices or sheets) and a large core, so that they fold up correctly! See the puzzle comments for Objective details.
Categories: Design, Overall

Top Groups

RankGroupScorePoints
1Go Science13,531100
2Anthropic Dreams13,50368
3Contenders13,33244
4Gargleblasters13,20327
5Beta Folders13,19216

Top Evolvers

Top Soloists

RankPlayerGroupScorePoints
1Dudit 53 52 Go Science13,501100
2sallallami 70 6  13,42196
3grogar7 38 2 Anthropic Dreams13,36392
4Enzyme 70 19 Gargleblasters13,19988
5LociOiling 4 1 Beta Folders13,19084


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Comments

bkoep's picture
User offline. Last seen 1 hour 5 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

DDG Metric (max +2000)
The predicted binding energy of your design. The goal DDG is -40.0 or less.

Contact Surface (max +2000)
Measures how much of your binder surface is in close contact with the target protein. The goal Contact Surface is 500 or more.

Buried Unsats (max +500)
Penalizes 100 points for each polar atom that cannot make any hydrogen bonds.

Core Existence (max +1500)
Ensures that at least 25 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.

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.

SS Design (max +500)
Disabled use of CYS residues. Penalizes GLY, ALA residues in sheets and helices.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons