Through the eyes of a scientist - Puzzle 1018
Baker Lab scientist bkoep recently sat down with Foldit players' designs from Puzzle 1018 for a visual inspection, which is the first step in our analysis of Foldit designs. Join us as we take a critical look at the latest symmetric proteins designed by Foldit players and voice some thoughts about the really cool things Foldit players are demonstrating in protein design!
In the video, you'll also hear brief discussion on the following topics:
- hydrogen bond networks
- core packing
- hydrophobic interfaces
- special considerations when designing with GLY, CYS, and MET residues
We apologize for the inconsistent sound quality—subtitles can be accessed on YouTube with the "CC" button below the video frame.
Check it out and leave your questions in the comments below!( Posted by bkoep 76 864 | Tue, 12/16/2014 - 00:56 | 14 comments )
Help us to solve a Vascular endothelial growth factor protein!
Vascular endothelial growth factor (VEGF) is a protein released to trigger new blood vessels to form. This is important in embryonic development and when healing from cuts and damage, but it can also be hijacked by cancer cells to trick the body into providing extra blood vessels (angiogenesis).
Puzzle 1012 comes from the VEGF receptor (type 1). The receptor forms a membrane dimer, with an extracellular part that binds VEGF and an intracellular kinase domain which is responsible for signaling. The extracellular portion consists of seven Immunoglobulin-like (Ig) domains. This puzzle consists of the sequence for domain 6.
Some experimental data has been collected for the VEGF receptor, but it hasn't yet lead to a finished structure. The hope is that if you can help us find near-native solutions then your Foldit predictions can be used to improve the structure. That in turn could lead to a better understanding of angiogenesis and eventually to new anti-cancer treatments.
Please try out the first puzzle for this unsolved protein here .
UPDATE: try out the second puzzle for this unsolved protein here .( Posted by beta_helix 76 1220 | Wed, 11/12/2014 - 20:18 | 1 comment )
Exploit found in puzzle 1000
A few players have pointed out a small problem in puzzle 1000 that can be exploited to get a few extra points: if the non-designable residues at the start and end of the peptide are deleted, and then reinserted, they become designable, meaning that you can now design five positions instead of the intended three. We don't think that this will invalidate the scientific results from this puzzle, so rather than re-post it, we are announcing the exploit so that no one has an unfair advantage. Feel free to design all five positions using this exploit.( Posted by v_mulligan 76 2145 | Thu, 10/23/2014 - 00:39 | 0 comments )
Foldit September Media Wrapup
We're at the end of September, and Foldit's been name-checked and featured in a fair number of places. Due to circumstances, I felt this great roundup post would help you find everything in an efficient fashion, as well as give a reason to re-announce what's coming up.
Coming up! Our next Science Chat on October 16, followed by a Developer Chat in December.
What's back: Our Demographic Survey 2014, new and improved. Help us collect those sweet stats, and please point all your group members towards it, because we lost everything (survey wise, that is). Combined with our recent puzzle survey, we are committed to helping drive our mission for great science side by side with good game fun, so please do take a minute or two to assist.
From the news side of thing, let's take a scroll back through September!
* The Guardian asks, "Could a game change your bad habits?"
* C&EN's Virtual Symposium 2014: Advances in Drug Discovery and Development featured Dr. David Baker's talk on "Design of Protein Structures, Functions and Assemblies". You have to register, but the streaming talk is free to listen for the next couple months.
* Seattle Times pointed out our role in Ebola research in "From donors to research, state has key role in Ebola fight".
* Scientific American magazine wrote an article titled "Citizen Science Is Stimulating a Wealth of Innovative Projects" and we're in there.
* We led this list in a sci-tech feature on crowd-sourced computing via the student newspaper at McGill University called "Harnessing the world's computational power".
* Al Jazeera America's video asks "Can Ebola video game help find cure for the deadly virus?"
* We were also part of the NSF's "Throwback Thursday" quiz in early September.
All about the recent downtime
Welcome back from the downtime, in which Foldit’s database attempted to pretend most of September did not happen. We know better and we know how hard and inconvenient it has been!
A database backup failed resulting in a loss of three weeks worth of data. This was discovered during our Wednesday maintenance.
What data was lost?
- Scoring for the last three weeks has been affected, and extremely likely to be unrecoverable.
- If you made an account on or after September 3, it is gone. Please remake your account, we want you to enjoy Foldit! (And are sorry for the extra hassle.) However, please do not pick the exact same name when you recreate your account. We cannot guarantee if you use the same name that you will be able to access chat, download recipes. Also some other functionality may be impacted. Take this opportunity to make a fresh new start. This is a known issue.
- All the demographic survey was lost. This means if you filled it out, we will need you to fill it out again. Yes, some slight improvements were based on initial feedback!
- Any news that was posted on the main site has been lost, but that just gives me an excuse to do a fabulous September wrap-up post.
What was not lost?
Scientific data was not lost.
What are we doing to help?
We can recreate puzzles after the servers come back up so you can not only play but share your solutions.
How you can help!
- Point your group members to this post.
- Tell everyone we’re back and ready to get back to the cool science.
- Report any and all NEW bugs in our thread here (hint: if there’s a feedback for that, it’s not new). Create feedback (after searching) with as many steps as you can so we can recreate your issue.
Thank you all for your patience - we know it hasn’t been easy and we’re all looking forward to getting back to doing great science!( Posted by inkycatz 76 2145 | Sat, 09/27/2014 - 04:08 | 30 comments )