The DU Folding@Home team - Alzheimer's, CJD, ALS, AIDS, Huntington's, Parkinsons and cancer research

[Agony]

"Help Stanford University scientists studying Alzheimer's, Huntington's, Parkinson's, and many cancers by simply running a piece of software on your computer.

The problems we are trying to solve require so many calculations, we ask people to donate their unused computer power to crunch some of the numbers."

There are 9 DUer's currently using spare CPU cycles to solve protein folding scenarios. The DU team is number 254 in the project
if you are interested -----> http://folding.stanford.edu
here is a link to the DU Folding@Home team statistics --> http://folding.extremeoverclocking.com/team_summary.php?s=&t=48157

Don't forget to join team#48157 when you sign up!

"What is protein folding?
Proteins are biology's workhorses- its "nanomachines." Proteins help your body break down food into energy, regulate your moods, and fight disease. Before proteins can carry out these important functions, they assemble themselves, or "fold." While protein folding is critical and fundamental to virtually all of biology much of the process remains a mystery.

When proteins do not fold correctly (misfolding), there can be serious health consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, AIDS, Huntington's, Parkinson's disease, and many cancers.

If we better understand protein misfolding we can design drugs and therapies to combat these illnesses."

Cheers,
Agony

[hobbit709]

1. I'm trying

http://fah-web.stanford.edu/cgi-bin/main.py?qtype=teampage&teamnum=048157

[Agony]

2. It will be a long time before I catch up with you!

you had your 7th anniversary on May 6th!

I need to figure out how to fold smaller work units so I can catch your ass!

[hobbit709]

3. Not sure how I got so many

I pretty much left it at the standard defaults when I set it up. I have 4 computers that I'm running folding on. Each has the basic client, the SMP client, and the NVidia graphics client running. Of course on those four computers I have a total of 30 cpu cores., so it doesn't usually bog down while I'm doing anything else on the computer.

[Agony]

4. I'm running simulations that look at protein folding inside the exit tunnel of the ribosome

Project 7809

These projects simulate protein folding inside the exit tunnel of the ribosome.

The ribosome is a large protein/RNA molecule that is used to translate mRNA into a protein. It does this by successively adding amino acids which correspond to codons in the mRNA sequence. Once these amino acids have been added to the chain, the peptide is extruded through a tunnel inside the ribosome, which is about ten nanometers long.

In an extended conformation (i.e. the peptide is completely stretched out) it would take ~30 amino acids to span the tunnel's length. This means that for the first part of the protein's life it is folding inside a tunnel!

Most modern protein folding experiments and simulations do not directly attack this phenomenon. We intend to explore the protein folding process within the ribosome tunnel in an attempt to look at protein folding as it happens in the cell.

This project simulates a 39 residue peptide within the exit tunnel.

[Agony]

5. right now I am running an src kinase simulation, an enzyme potentially responsible for cancer

Project 8082

The Src family protein tyrosine kinases are enzymes that play key roles in transducing cellular signals regulating cell growth, differentiation, proliferation, migration and survival. These enzymes are responsible for diseases such as cancer in which the cells undergo uncontrolled differentiation. Crystallographic x-ray structures of human c-Src in the inactive and active conformation allow clear structural distinctions to be drawn between the inactive and active states. Those x-ray structures, though rich in information about the two end-points of the activation event, do not show how the activation occurs and how it might be regulated. Simulations and computational models, at different levels of approximation, can complement some of the missing information about Src and help address these important questions. Characterizing conformational transitions in large biomolecules such as Src is challenging, however, because the slow processes are not easily observed during simple unbiased molecular dynamics (MD) simulations. To circumvent those difficulties, previous studies of Src by our collaborators have used biased sampling techniques such as string method to get the series of structures which show the structural changes involved in the activation process. In this project, we perform simulations of src kinase from the structures obtained using the string method to get a more detailed picture of the activation process.

[Logical]

6. I just joined! Old laptop but still hope it helps! n-t

[Agony]

7. i've been running F@H on and off for 4 years after DU'er alfredo did an OP like this one

tip-o-the-hat to alfredo!

You can configure it to use as little or as lot of your CPU as you want. I just got a different computer and I am running F@H full out to see what it can do. (and try and catch up to Hobbit709)

Cheerio!
Agony

[Agony]

8. just assigned a new work unit - simulating difference between in vitro and in vivo protein folding

Project 7808

These projects simulate protein folding inside the exit tunnel of the ribosome.

The ribosome is a large protein/RNA molecule that is used to translate mRNA into a protein. It does this by successively adding amino acids which correspond to codons in the mRNA sequence. Once these amino acids have been added to the chain, the peptide is extruded through a tunnel inside the ribosome, which is about ten nanometers long.

In an extended conformation (i.e. the peptide is completely stretched out) it would take ~30 amino acids to span the tunnel's length. This means that for the first part of the protein's life it is folding inside a tunnel!

Most modern protein folding experiments and simulations do not directly attack this phenomenon. We intend to explore the protein folding process within the ribosome tunnel in an attempt to look at protein folding as it happens in the cell.

This project simulates a 39 residue peptide within the exit tunnel.


Technical details

This project (p7808) is set for 1698.09 points, a preferred deadline of 25.23 days, and a final deadline 54.66 days. This project uses the GRO_A4 FAH core software and is hosted by Folding@home server 171.64.65.99.

Manager for this project

Christian Schwantes is a Graduate Student in Vijay Pande's group at Stanford University. He is interested in protein folding, but he is most interested in how protein folding in a cell is different than folding in a typical experiment or simulation.

The conditions are very different when comparing in vivo (i.e. in a cell) to in vitro (i.e. in a test tube) folding. For example:

1) Protein folding can occur co-translationally. This means that the protein can fold as it is being synthesized

2) Proteins in the cell are surrounded by a lot of things, like salts and chaperones, which can have a profound effect on the folding process

For these reasons, Christian would like to explore the folding process in the cell, which can hopefully provide new insight into the protein folding problem.

[Agony]

9. Project 8084 - simulations of src kinase enzymes responsible for diseases such as cancer

Project Description:
The Src family protein tyrosine kinases are enzymes that play key roles in transducing cellular signals regulating cell growth, differentiation, proliferation, migration and survival. These enzymes are responsible for diseases such as cancer in which the cells undergo uncontrolled growth and proliferation. Crystallographic x-ray structures of human c-Src in the inactive and active conformation allow clear structural distinctions to be drawn between the inactive and active states. Those x-ray structures, though rich in information about the two end-points of the activation event, do not show how the activation occurs and how it might be regulated. Simulations and computational models, at different levels of approximation, can complement some of the missing information about Src and help address these important questions. Characterizing conformational transitions in large biomolecules such as Src is challenging, however, because the slow processes are not easily observed during simple unbiased molecular dynamics (MD) simulations. To circumvent those difficulties, previous studies of Src by our collaborators have used biased sampling techniques such as string method to get the series of structures which show the structural changes involved in the activation process. In this project, we perform simulations of src kinase from the structures obtained using the string method to get a more detailed picture of the activation process. This project is similar to FAH projects 8041 and 8042.