1986: Biotin Ligand Binder Design

Status: Closed

Summary

Name:	1986: Biotin Ligand Binder Design
Status:	Closed
Created:	04/28/2021
Points:	100
Expired:	05/05/2021 - 23:00
Difficulty:	Intermediate
Description:	Design a binding pocket for the biotin ligand! Biotin is an important vitamin, and is necessary for the regular function of many metabolic proteins. One bacterial protein called streptavidin binds to the biotin ligand extremely tightly. The biotin-streptavidin pair is well known for being one of the tightest ligand-binding interactions in all of biology. We'd like to design proteins that can bind ligands just as tightly, but this is a difficult protein design challenge. The streptavidin protein has a binding pocket that fits closely around biotin ligand and satisfies all of its buried polar atoms, and this is essential for the tight binding between the two molecules. In this puzzle, players are challenged to design a binding pocket for biotin. We've provided the streptavidin backbone as the starting structure, but players can 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

Thu, 04/29/2021 - 00:39

#201

bkoep 75 288

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.

Thu, 04/29/2021 - 01:09

#202

OWM3 75 1437

Offline

Joined: 03/08/2020

Groups: Gargleblasters

The puzzle looks broken.

Thu, 04/29/2021 - 01:13

#203

OWM3 75 1437

Offline

Joined: 03/08/2020

Groups: Gargleblasters

Whatever

You may ignore this comment, I had to restart my foldit instance to fix a damn glitch :)

Thu, 04/29/2021 - 04:35

#204

spdenne 75 402

Offline

Joined: 10/01/2011

Groups: Void Crushers

This puzzle crashes (on windows)

****** Encountered Crash at ..\..\..\source\src\core\chemical\ResidueType.cc:4071
unknown atom_name: ' CA ' in residue BTN

Thu, 04/29/2021 - 22:58

#205

milkshake 75 1437

Offline

Joined: 07/17/2019

Groups: Foldit Staff

Thanks

Thank you spdenne, we have a lead on how to fix this.

Thu, 04/29/2021 - 23:41

#206

milkshake 75 1437

Offline

Joined: 07/17/2019

Groups: Foldit Staff

In the meantime, disabling

In the meantime, disabling the view option "Show backbone issues" should prevent the crash.

Fri, 04/30/2021 - 05:42

#207

spdenne 75 402

Offline

Joined: 10/01/2011

Groups: Void Crushers

Thank you

for the work-around

Fri, 04/30/2021 - 21:56

#208

spvincent 30 12

Offline

Joined: 12/07/2007

Groups: Contenders

Its hard to do much redesign

Its hard to do much redesign when you can't add or delete segments.

Sat, 05/01/2021 - 01:24

#209

bkoep 75 288

Offline

Joined: 11/15/2012

Groups: Foldit Staff

That's good to know!

We probably don't want to allow extra residues in these puzzles. But in future puzzles we should be able to allow deletions and re-insertions.


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