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425: H2N2 Flu Design Puzzle 1
Status: Closed


Name: 425: H2N2 Flu Design Puzzle 1
Status: Closed
Created: 05/28/2011
Points: 150
Expired: 06/05/2011 - 02:00
Difficulty: Intermediate
Description: This is the first of the many new exciting Flu puzzles David Baker mentioned in his blogpost. Our lab designed against the H1N1 subtype of the virus, but a related subtype with pandemic potential, H2N2, has different sidechains in this region that perturb binding. The goal is to design the interface of these designs so that it can bind to the H2 subtype of Influenza. This puzzle is worth 150 global points! If you are new to Foldit, make sure you have completed the Intro Puzzle 4-5 and Design Puzzles 6-1 through 6-4.
Categories: Design, Overall

Top Groups

3Russian team7,73897
4Void Crushers7,73177
5Anthropic Dreams7,72961

Top Evolvers

1Mark- 62 2044 Contenders7,741150
2mimi 62 2044 Contenders7,740147
3deus911 62 103 foldeRNA7,733143
4Fat Tony 62 2044 foldeRNA7,731135
5wld333 62 2044 foldeRNA7,731131

Top Soloists

1marie_s 62 2044  7,740150
2BootsMcGraw 13 7 Contenders7,740147
3vertex 62 2044 Contenders7,739143
4wld333 62 2044 foldeRNA7,739139
5Grom 62 468 Russian team7,738135

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beta_helix's picture
User offline. Last seen 18 min 8 sec ago. Offline
Joined: 05/09/2008
Groups: None
This puzzle requires the latest update

In order to play this exciting puzzle (worth 150 global points) make sure to download the latest update (it should download automatically when launching Foldit).

Joined: 08/06/2010
Groups: Contenders
flexible vs. locked

When 425 finishes, are you going to re-release the top 8 or so mutation combinations in an alignment puzzle without the locking of the mutated backbone?

I mean it is unrealistic to think that we can mutate long segments of this drug without affecting the shape of the secondary structures we are mutating, right? I believe that unlocking those structures would really help us to help you to design a better bonding drug.

What is the intent of allowing those segments to mutate without allowing them to be flexible?

Joined: 05/09/2008
Groups: Void Crushers
Why are the backbone scores

Why are the backbone scores for segments 305 and 317 so bad?

I have a backbone score on 305 at the moment as -1999 and 317 as -2000. There is no way to improve this as they are locked.

This can't be the natural state for them, can it?

beta_helix's picture
User offline. Last seen 18 min 8 sec ago. Offline
Joined: 05/09/2008
Groups: None
Re: TheGUmmer

Those crazy scores are due to the constraints on both those key amino acid sidechains.

As you mentioned, all the backbone values are fixed so there is no way to improve them (but as you probably noticed, due to the constraints on them you can make both scores worse by pulling 305 and 317 too far away ).
These bad initial scores are constants and are simply artifacts of the constraints, they do not represent anything wrong with the topology of the drug and score perfectly fine without the constraints.

You'll be able to see this in future versions of this Flu puzzle (to answer saksoft2's question) when we allow you to modify parts of the structure.

saksoft2, we wanted to start with a more conservative initial puzzle rather than let you change everything only to have the top solutions all come back with a giant helix or something ;-)

Ideally, if a Foldit player can come up with a single design that binds H2N2 and it is also able to bind other subtypes that would be perfect, right?

itskimo's picture
User offline. Last seen 9 years 25 weeks ago. Offline
Joined: 08/10/2010
Groups: foldeRNA
the effects of 2 point evo ?

looks like the groups were spread more evenly across the score board. I hope this is a good thing ? :)

deus911's picture
User offline. Last seen 4 days 18 hours ago. Offline
Joined: 05/11/2008
Groups: foldeRNA
"Super antibody' fights off flu" - FI6


Wanted to mention it since it's related.

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