New client/protein performance?

[Galuvian]

This is mostly for Howard or anyone ele familiar with the science behind this project. The educational forum hasn't had any activity for months. I'd be really curious to get some updated information since we've moved to this new stage.

There is a huge increase of production with the new protein, how much of this increase is due to the smaller size? At the current rate, we're going to hit 1 billion structures in about 10 days. It took a month with the previous protein. Is this a particularly 'easy' protein to be working on?

Stage 2 appears to be producing significantly lower RMSDs. The educational forun has some forumulas for predicting the lowest RMSD, and we seem to be beating the pants off of that.

Just following the stats page, it appears that the lowest RMSDs are showing up within the first 100 million, and any improvement beyond that will be very small. Is that true? What are the implications of this? Are we going to continue running 1 billion just in case there is a lower one produced? I know that following just the top 10 isn't much of an indicator for the entire spectrum of RMSDs being produced, but our goal is to find the lowest one we seem to be getting there.

I've seen posts by a few people feeling upset that we are 'cheating' to figure out the lowest RMSD. I don't share those feelings because I understand why it is being done, but I'm really curious about what needs to happen before the project is predicting which ones will be the lowest on it's own?

My final question is slightly less related to the DF project. I saw a lecture on public television the other night by a professor at UCSF whose name escapes me. The lecture was from mid-2002. He had been doing research on Prions. My question is, are the medicines DF is trying to help create related to these prions or are they separate branches of trying to figure out how proteins work?

-Galuvian

[Brian the Fist]

A lot of your questions are answered in the Phase II FAQ on the web site (http://www.distributedfolding.org/phaseiifaq.html)

Prion proteins sometimes fold incorrectly and lead to disease conditions. Yes, understanding protein folding will help understand how and why prion proteins misfold, and how this can be corrected/prevented. As we've said in the past, we are doing basic research here though. We are not 'curing cancer' or finding AIDS drugs, we are at a much more basic level, trying to understand the science/physics behind protein folding. A better understanding of the process will benefit many diverse fields in the biological sciences, not just one, and will server as a basis for others to solve more specific biological problems from.

If you have any questions after reading the FAQ still, please dont hesitate to ask.

[Galuvian]

The only question I asked that is even close to being answered in the phase II FAQ is about performance, but the questions I'm asking is different.

Sorry if I sound blunt, I'm fighting tendinitis and I've already done more typing than I should for today.