Update on biomedical research projects foldIt players will be contributing to
I have been describing some of the projects being carried out in my research group on my rosetta@home page; this may be of interest to some of you.
With the exciting new design release coming up, you will soon be able to contribute directly to these and many other projects by playing foldit puzzles!( Posted by David Baker 74 1963 | Thu, 03/12/2009 - 05:30 | 0 comments )
Sneak Preview: Custom Tools (Macros)
We are approaching the release of another foldit feature that may well change the very fabric of the game. Up until now, we have been evolving the tools in order to adapt to the way players tend to manipulate proteins, and according to the way expert biochemists would like to alter the configuration.
In the spirit of allowing you to shape the course of scientific research, we've been planning to do something much more powerful: allow you to design, share, refine, discuss and rank new tools by combining the low level building blocks into more complicated operations through a simple visual interface. We are currently working on making the scripting process accessible to gamers who have never programmed before, in hope that all of you will explore this exciting new space. Here's the snapshot of our visual scripting interface:
The macros will first be released for individual use. we will subsequently release the ability to share, rank, edit, and see the analytic value of each macro (for example, you can find out that people who have used a specific macro have scored 20% higher on the previous 3 puzzles than the people who did not). We think that this tool exploration will enable discovery of brand new protocols that could also enable computers to perform better. Heck, biochemists have published numerous articles just on the discovery of such new protocols. I'm betting that the folding community can do just as well if not better at discovering new strategies to efficiently fold proteins.
Sneak Preview: HIV Design Game
We are approaching a release date for our first protein design game. In these classes of games, you will still fold proteins, pack them in the smallest possible places, bury the hydrophobics, etc. In addition you will be able to craft different parts of the protein in order to achieve secondary goals. For example, an additional goal could be that the external shape of the created protein fits very nicely with a virus, or any other molecule.
You will be crafting proteins by changing the actual amino acids anywhere on the backbone, and even extending the protein sequence. There will be a few new tools, and even some additional requirements for a successful design aside from the score. To get you ready to make your own proteins we will be introducing new set of level puzzles specifically focusing on protein design.
We are particularly excited about this new chapter in foldit evolution because there are practically no automated methods for protein design -- you will be primarily competing with the biochemistry experts to find the best novel protein structures. In my view, I think foldit players will likely provide even greater advancement to science with design problems. The best part is that each set of puzzles will be focusing on a different target, such as an HIV virus. The best scoring proteins will then be synthesized in the biochemistry lab in order to confirm it's folding structure and the protein function. The biochemists focusing on the specific problems will keep us all up to date with the findings. These findings in turn will produce new design puzzles for us to work on. Effectively, you will all be the crucial part of the scientific exploration process!
The first design puzzle will focus on the HIV virus. Some time around the release date, we will introduce you to the biochemist who will describe the objective, and the scientific hypothesis you will be working on. The tentative release date is second part of March.