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2037: Cortisol Ligand Binder Design with AlphaFold Predictions
Status: Closed

Summary

Name: 2037: Cortisol Ligand Binder Design with AlphaFold Predictions
Status: Closed
Created: 08/27/2021
Points: 100
Expired: 09/03/2021 - 23:00
Difficulty: Intermediate
Description: Design a binding pocket for the cortisol ligand! This puzzle enables AlphaFold predictions for your binder design, so you can upload your solution for AlphaFold using the AlphaFold prediction tool. AlphaFold will predict the structure of your binder only (i.e. in the absence of the ligand). If you load this prediction, then Foldit will attempt to align the prediction with your solution. If you continue working off of the AlphaFold prediction, you may need to make adjustments in the binding pocket where the ligand makes contact with your binder design.

Cortisol is a natural signaling molecule that the body uses to regulate metabolism and inflammation. Commonly known as a "stress hormone," cortisol levels tend to increase under conditions of chronic stress. We'd like to design a cortisol binder that could be used to detect the hormone or sequester it from the blood stream. Cortisol is mostly hydrophobic, but has several polar atoms that need to be satisfied by H-bonds in the binding pocket!

In this puzzle, players are challenged to design a binding pocket for cortisol. We've provided a generic NTF2-type backbone as the starting structure, with the cortisol ligand placed roughly in the correct position in the binding pocket. However, players may completely redesign the protein or reposition the ligand within the binding pocket. Try to design a binding pocket with high Contact Surface and zero BUNS! See the puzzle comments for Objective details.
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 25 min 53 sec ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Contact Surface Metric (max +2000)
Measures how much of your binder surface is in close contact with the target protein. The goal Contact Surface is 200 or more.

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

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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