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.
First chat time
It seems that our players are all over the globe, so we'll just try to have chat sessions at different times of the day until we converge to a regular time. Over the weeks, I'll make sure that you get to pick the brains of other members of our dev team, especially Seth Cooper (foldit is his PhD thesis), our newly formed satellite dev team in Pittsburgh, as well as David Baker and folks from this lab.
The first chat is scheduled for Thursday 8:30pm PST.
See you there!
Today's Downtime and Poll for Possible Chat Sessions Times
It looks like we survived the update of our database, file server and web clients today. the new setup should allow us to scale up to the additional protein design challenges, and allow us to expand the game so that you can design your own tools and protocols for refining proteins (more on that in the upcoming blog post).
It has been suggested several times that we're falling short on "customer support" aspect of this project. We have to agree with you on this. It's simply a tradeoff between all the things we have to do to move this project towards eventual scientific discoveries and all the things that our players would like us to do.
To demonstrate that we listen to your suggestions, we'll setup specific times where developers will be available for the in-game chat. We'll log these chats and have a special place for them on the web site.
So my question is what might be the best time to hold such a chat session? Make yourself heard below and we'll try to schedule something as long as it is within the reasonable hours in PST time zone.
A brief message about the Rosetta Energy Function
I just wanted to show an example of the Rosetta energy function that is used in Foldit.
We have evidence that the Rosetta energy function is able to pick out the native conformation when compared to many other models.
In the attached plot, the y-axis is the Rosetta score (negative is better here) and on the x-axis is how far off the model is from the native (so closer to the left is better). The wiggled native proteins are shown in blue on the very bottom left with all the black dots representing Rosetta predictions.
If you were to look at all models with a Rosetta score of exactly -170 (draw a line horizontally across the graph at -170) you can see that these models are very different from one another. If you look at the most successful predictions (shown by the red arrow) you can see that they have the best Rosetta score and are closest to the correct native structure. Based on this, we believe that our energy function is good at picking out folds that are similar to the native.
You'll notice that most of the Rosetta predictions on this graph are far from the native structure.
We are hoping that Foldit players will be able to more efficiently make accurate models of protein structures, because the automated methods are essentially random searches.
This figure is taken from the Science article:
"Toward High-Resolution de Novo Structure Prediction for Small Proteins"
Philip Bradley, Kira M. S. Misura, and David Baker
Science 16 September 2005: 1868-1871.
Exciting preliminary results in Grand Challenge puzzles!
First of all, I would like to thank all of you for participating in this most exciting new venture! I think FoldIt has real promise for making it possible for people all over the world and from all different backgrounds to bring their talents and unique skill sets to bear on solving critical problems in biomedicine and bioengineering. And of course, have fun at the same time!
My research group at the University of Washington has been working on the protein structure prediction problem for quite some time. With the Rosetta program and the computing power of Rosetta@home, we can now predict structures accurately for small proteins. The main obstacle preventing us from being able to predict structures of larger and more complex proteins is that finding the correct structure becomes increasingly difficult. The correct structure almost always has lower energy than incorrect structures, so if Rosetta can locate the native structure it can be identified based on its very low energy. We find that Rosetta often gets close to the native structure, but not close enough for the energy to drop significantly. This drop requires a last few twists and contortions that Rosetta, which searches by making random changes and evaluating the energy, is not smart enough to try.
The Grand Challenge puzzles are testing whether FoldIt players can overcome these last obstacles which Rosetta often fails at. The starting points in these puzzles are generally pretty close to the correct structure, but there are one or a small number of errors which prevent the energy from dropping (in FoldIt, to get a score more like a traditional computer game, we take the negative of the energy, so a higher score means lower energy).
The exciting preliminary result is that many of you are able to recognize the problems in the starting structures--many of which are the structures that Rosetta trajectories got stuck at==
and fix these problems remarkably well. Over the next month we will be releasing more puzzles with different types of errors in the starting Rosetta generated structures, and doing a full analysis of the results on these challenges which we will report to you directly and to the world via a scientific publication. Beginning with the central issue of whether human intelligence and intuition can overcome obstacles hindering computers from solving problems like protein folding, here are many fascinating questions, most of which have never been considered before.
Keep up the great work!
David( Posted by David Baker 91 2622 | Mon, 01/26/2009 - 06:39 | 5 comments )