New Release Soon
There's a small change to both devprev and main that will go out soon. It fixes an issue with logging so there will be no changes that you see on your end.
We're still working on the issues you guys brought up in the devchat and more. Those changes should go out in the next release.
Thanks everyone(Tue, 03/26/2013 - 17:43 | 0 comments)
Design puzzles and progress update
Your de novo protein designs are looking extremely good! Our goal since we introduced design puzzles was to have the best solutions go straight into experimental testing. This requires synthesizing a gene encoding the design, putting the gene into bacteria to direct them to make the protein, and then purifying the designed protein away from everything else in the bacteria and determining whether it folds up the way you designed it to. As you can imagine, this involves a fair amount of effort, and up until recently there have been issues with the top scoring designs that would have had to be fixed before ordering the genes.
What are the issues that we would like to resolve before ordering your designs? There are several “rules of thumb” about proteins that earlier designs were not consistent with. The main one is very simple and familiar to most of you-in proteins the buried residues should be hydrophobic and the exposed residues should be polar. Another perhaps less familiar one is that glycine residues, which are very flexible, should only be in turns and loops, not in helices or sheets. Finally, there should be few alanine residues in the core because they are too small to stabilize the protein much.
The filters which have been added over the past month or two simply enforce the above rules. You might wonder why the score function itself doesn’t take care of these problems. The answer is that naturally occurring proteins break all the rules some of the time-nature had 3 billion years to fine tune things and can get away with things that designers simply can’t. If we encoded the rules directly in the score function, we would fail to correctly predict the structures of many native proteins.
The exciting result is that the top designs now do not break the rules, and so are close to being ready to order. On the other hand, there are clearly problems with the filters that make the game less fun to play, and we are working hard to fix them. The main issue is that they are slow to compute, but I think this can be fixed pretty easily (the way we are determining whether a residue is buried is more time consuming than it needs to be, for example).
So please keep designing, and we will work hard to improve speed. I’m really excited about the beautiful symmetric structures you are creating and can’t wait to start testing them. If the sequences of your designs fold up to the structures you have created it will be a major scientific milestone! There will be immediate applications, for example to stabilizing the HIV surface protein, which is a trimer, in a form which can be used as a vaccine.( Posted by David Baker 140 4559 | Mon, 03/25/2013 - 16:27 | 1 comment )
Devchat 3/25 11:00am PDT
Get your questions ready, folks. It’s time for a devchat! Come chat with our developers in #global this Monday 3/25 from 11:00am-12:00pm PDT / 18h00-19h00 GMT. We’re on Pacific Daylight Time here in Seattle (-7 GMT) so don't forget to double check your time zone conversion. A transcript will be available on the site after the chat for those who can't make it.
If you need help getting into #global chat, check out this helpful guide for assistance.
Thanks and we’ll see you there!
Edit: A transcript is now up for those of you who missed Monday's chat. Thanks!
- katfish(Fri, 03/22/2013 - 23:07 | 4 comments)
New position open - System Administrator
Happy Friday, folders!
We have a new opportunity for you to come work with the creators of Foldit. We are currently seeking a System Administrator to work on Foldit and other Center for Game Science titles. Know a good candidate? Send 'em our way.
Our new System Administrator will be helping us make sure our servers continue to run smoothly -- no more surprise crashes!
- katfish( Posted by katfish 140 1871 | Fri, 03/15/2013 - 21:05 | 0 comments )
We've just pushed the changes that were in the developer preview into the main game. There is a small change in devprev as well. You will need to use this new version for future design puzzles. Here is the full list of changes:
- Intro puzzle level number shows up in title.
- A new checkbox has been added to the behavior panel that allows you to disable slow filters
- bool behavior.GetSlowFiltersDisabled()
- void behavior.SetSlowFiltersDisabled(bool setting)
* Bug Fixes
- The behavior panel will now properly update when opened if options were changed from scripts
- Showing isosurface on puzzles with multiple chains will now work
* LUA structure.GetAminoAcid() / get_aa()
- Virtual residues will now return 'vrt'
- Sugars will now return 'unk'
- DNA will now return 'da' for "ADE", 'dc' for "CYT", 'dg' for "GUA", and 'dt' for "THY"
- RNA will now return 'ra' for "RAD", 'rc' for "RCY", 'rg' for "RGU", and 'ru' for "URA"
* LUA structure.GetSecondaryStructure() / get_ss
- Will return 'M' instead of '_'
The new 'Disable slow filters' check box should be especially helpful in the design puzzles that utilize filters - checking it will make the game run much faster, but you'll have to uncheck it before you can post scores again.
Scoring the protein properly takes time, and we need to score it properly for things to be fair and scientifically useful. However, we don't need to be recalculating this filtered score all the time, which is why we've given you the option to temporarily disable the slow filter scoring.(Thu, 03/14/2013 - 21:09 | 5 comments)