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 122 354 | Sat, 09/27/2014 - 04:08 | 31 comments )
New anti-Ebola puzzle posted
Based on player feedback, we've posted another design puzzle to create a peptide inhibitor of the Ebola glycoprotein, this one with 30 amino acid residues. The puzzle is live now, and expires just before the scheduled server downtime on Sept. 3rd. Bonne chance!( Posted by v_mulligan 122 1223 | Wed, 08/27/2014 - 21:26 | 0 comments )
Continuing the battle against Ebola
As you know, the current Ebola outbreak in Western Africa has now claimed over 1,000 lives, making it the worst Ebola outbreak to date. Currently, no proven treatment or vaccine exists to combat Ebola. It has been some time since our last Ebola design puzzles (http://fold.it/portal/node/997612 and https://fold.it/portal/node/997525) were posted. These, in combination with the initial hotspot-finding puzzle (https://fold.it/portal/node/996919), have both yielded some great leads that we are currently working to test in the wet lab. In particular, some of the best player hotspots yielded excellent starting points for the design of small, cyclic peptides that we're quite excited about.
The process of going from a candidate design to a drug ready for deployment in the field is a long one. We start by screening a large number of candidates for binding to the Ebola surface glycoprotein, using high-throughput methods. Because the Ebola virus is obviously quite dangerous, we can't work with it ourselves in our wet lab. We therefore use Ebola proteins that have been made in harmless strains of bacteria, using recombinant DNA technology. As for the candidate designs, we express these in baker's yeast, also using recombinant techniques. Because we are using high-throughput methods at this stage, we expect some false positives from our screen. Some candidates, for example, are just generally "sticky", and bind to pretty much anything. These would not be useful as drugs, since they'd stick to all sorts of other things in the body, but they show up in the initial screen as a hit.
Once we have some possible hits from our initial screen, we express and purify larger amounts of these second-round candidates for more careful experimental validation using lower-throughput techniques. At this stage, we need to do careful controls to confirm that the second-round candidates aren't just generally sticky. We also start to get quantitative at this point, to see whether a design binds tightly enough to be a useful drug, or whether it needs further redesign to improve its binding affinity.
Through collaborators, we will ultimately test candidates that pass all of our tests in cell culture, then in animals infected with the virus. The road to human trials is longer still, since it's necessary to show that a drug is safe before it can be given to sick people. Even with a disease as horrible as Ebola, one has to be sure that the treatment isn't worse than the disease. We're not yet anywhere near the stage at which candidates could be administered to people suffering from the Ebola virus -- but with time, effort, and patience, we hope to get there.
In the mean time, now that CASP is winding down, we will be posting a few more Ebola puzzles in the next few days. In particular, I'm curious about whether players could do better than the automated algorithms at designing a heavily disulfide cross-linked peptide to bind to the Ebola glycoprotein... We look forward to finding out!( Posted by v_mulligan 122 1223 | Thu, 08/14/2014 - 04:32 | 0 comments )