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1431: Unsolved De-novo Freestyle 117
Status: Closed

Summary

Name: 1431: Unsolved De-novo Freestyle 117
Status: Closed
Created: 09/16/2017
Points: 100
Expired: 10/09/2017 - 23:00
Difficulty: Intermediate
Description: Note: In response to some player feedback related to the excessive size of this protein, we're extending the puzzle deadline by two weeks! The puzzle will expire on October 9 at 23:00 UTC.

Chikungunya (CHIK-un-goon-ya) virus (also known as CHIKV) is a mosquito-transmitted alphavirus that has spread around the world and is currently infecting people in about 60 countries globally. CHIKV is rarely fatal, but causes severe joint pain for months to years that can debilitate affected patients for long periods of time. There are currently no known drugs to treat CHIKV infection, primarily due to a lack of understanding of the structure of CHIKV proteins involved in viral genome replication. The Geiss lab has worked on developing drug targeting the membrane bound CHIKV nsP1 protein, which is the anchor for the viral genome replication complex on cellular membranes and a multifunctional enzyme that forms a 5’ RNA cap structure on the end of the CHIKV RNA genome. Solving the structure of the CHIKV nsP1 protein would provide critical information for designing drugs that inhibit nsP1 function and abort viral genome replication.

The structure of this protein is still unknown. Secondary structure predictions (from PSIPRED) are marked on the starting structure, and provide clues about where the protein might form helices and sheets!

Note: Since the protein is huge for Foldit, we have divided the protein into two puzzles. This is the first puzzle.

Sequence:
MDPVYVDIDADSAFLKALQRAYPMFEVEPRQVTPNDHANARAFSHLAIKLIEQEIDPDSTILDIGSAPARRMMSDRKYHCVCPMRSAEDPERLANYARKLASAAGKVLDRNISGKIGDLQAVMAVPDTETPTFCLHTDVSCRQRADVAIYQDVYAVHAPTSLYHQAIKGVRVAYWVGFDTTPFMYNAMAGAYPSYSTNWADEQVLKAKNIGLCSTDLTEGRRGKLSIMRGKKLKPCDRVLFSV
Categories: Overall, Prediction

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Comments

Joined: 08/10/2014
Jpred prediction
Joined: 09/21/2011
Groups: Void Crushers
alignment templates

On such a big puzzle, it might be an idea to give us a few templates to work with. That might give us a chance to get to a structure that might be close.

toshiue's picture
User is online Online
Joined: 01/31/2016
Groups: Go Science
yes!

yes!!!, please

Joined: 06/06/2013
Groups: Gargleblasters
have to abandon due to size

Just a note. I'd love to work this, but was out two days and don't have time to pull this together. sorry not to have more time, but little machine can't do this size puzzle in regular time period.
Maybe a little extra time for the next large puzzle would help
Skippy

Susume's picture
User offline. Last seen 6 hours 44 min ago. Offline
Joined: 10/02/2011
More time

I agree, on a puzzle this size we could really use a few extra days or even an extra week.

Enzyme's picture
User offline. Last seen 47 years 44 weeks ago. Offline
Joined: 07/10/2008
Groups: None
More time

Specifically large de-novo, my vote would be to run them for about 4 weeks

Susume's picture
User offline. Last seen 6 hours 44 min ago. Offline
Joined: 10/02/2011
A tip from homologs

There are a few homolog (related) sequences that form real proteins but that match only segments 49-175 of our target protein, with one or both ends of our protein missing. I'm pretty sure that means segments 49-175 should be able to fold into a realistic protein shape without the ends being present. The ends would then add on without disrupting the shape of the middle section (and without depending on each other, since either end can be present while the other is absent). I have tried a couple of tracks where I fold 49-175 first, then add the ends on, and they seem to be working out well.

Joined: 09/24/2012
Groups: Go Science
Templates

Then for a following round, researchers could provide us with several templates for seg 49-175 (as suggested by Timo). It would help focusing.

lamoille's picture
User offline. Last seen 3 days 15 hours ago. Offline
Joined: 09/21/2011
Scoring Issue ?

Just asking, but is there an issue in scoring this puzzle ? It expired 12 hours ago and still no scores have been posted. Thanks for any feedback.

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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, Microsoft, Adobe, RosettaCommons