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Stanford's goal: to understand protein folding, protein aggregation, and related diseases.



What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, and Parkinson's disease.

What does Folding@Home do? Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. Stanford uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct Stanford's approach to examine folding related disease.



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Potential Therapy For Alzheimer's
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,814,000
Work Units: 6,597

Posted: Mon Apr 29, 2013 03:21 pm
Things have been pretty quiet this month, but I did manage to find a few interesting articles on Alzheimer's.


Alzheimer's Gene Discovery Offers Hope For Preventive Therapy

Quote:
Alzheimer's disease is the most common neurodegenerative disorder, affecting more than five million Americans, but currently there is no way to prevent, delay or stop its progression. A study published online by the Cell Press journal Neuron shows that a gene called CD33 contributes to Alzheimer's disease by inhibiting the ability of immune cells to remove toxic molecules in the brain.


Full Article here



Potential Therapeutic Targets Revealed For Late Onset Alzheimer's Disease

Quote:
Scientists from the Icahn School of Medicine at Mount Sinai, in collaboration with researchers from Icelandic Heart Association, Sage Bionetworks, and other institutions, have discovered that a network of genes involved in the inflammatory response in the brain is a crucial mechanism driving Late Onset Alzheimer's Disease (LOAD). The findings, published online in the journal Cell, provide new understanding of key pathways and genes involved in LOAD and valuable insights to develop potential therapies for the disease.


Full Article here



Potential Therapy For Alzheimer's Disease Revealed By Gene Networks In Brains Of Deceased Patients

Quote:
Most information about the cause of Alzheimer's disease is based on studies from animal models. Now, a study published by Cell Press in the journal Cell examines the brain tissue of deceased human patients and sheds light on dysfunctions in molecular networks in the brain that are at the root of Alzheimer's disease.


Full Article here
FAH paper listed amongst best of 2012 by Biophysical Journal
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,814,000
Work Units: 6,597

Posted: Tue Mar 26, 2013 03:16 am
It's been a busy month at Stanford, one of their papers was listed among the best of 2012 by Biophysical Journal, OpenMM now has it's own youtube channel, a new GPU core was released, and the new FaHBench Tool was released.

Quote:
Biophysical Journal announced their "Best of 2012" paper collection. We were excited that one of our papers was included. That work, "Protein Folding is Mechanistically Robust" investigates how key aspects of FAH technology (MSMs) can yield new insights into protein folding in some unexpected ways. Congratulations to Jeffery Weber for his work. We've posted the technical abstract below as well.


Full Article here



OpenMM Youtube channel

Quote:
OpenMM is a key part of Folding@home, powering its GPU cores. You can learn more about OpenMM at its youtube page, which includes technical videos on how you can incorporate OpenMM into your code. It also includes an introduction to Markov State Models (MSMs), which is a key technology used in Folding@home.


Full Article here



Introducing Folding@Home Core 17 GPU zeta core

Quote:
As also announced on OpenMM/Folding@home programmer Yutong "proteneer" Zhao's web site, we are happy to announce that Folding@Home Core 17 has entered Beta. Externally, you probably wont notice too much of a difference. Internally, this is a complete overhaul that brings many new features, and sets a strong foundation for the future of GPU core development. In addition, the restructuring brings much tighter integration of the core with the rest of the development within Folding@Home.


Full Article here



FAH bench FAH core/OpenMM-based benchmark for your GPU

Quote:
As previously blogged, FAHBench is the official Folding@Home GPU benchmark. It measures the compute performance of GPUs for Folding@Home. In addition, by use of a loadable DLL system, it provides vendors and skilled hackers with a method make customized-plugins and test their results.


Full Article here



GPU core progress & general design philosophy

Quote:
We often have to make difficult decisions on what hardware to support in the future, including adding new platforms or removing existing ones. Removing existing platforms always leads to a lot of disruptive change for donors, so we try to do this as rarely as we can. In particular, in the GPU1 to GPU2 transition, there was a big change done quickly, which was extremely hard on donors.


Full Article here



FAHBench 1.0

Quote:
Weve released FAHBench 1.0, with a new slick GUI that should make it much more accessible to new comers. Click on the FAHBench link above or the image below to try it out! Dont worry, it maintains backwards compatibility with the old command line interface.


Full Article here



Peptoid structure prediction

Quote:
Guest post from Dr. Greg Bowman, UC Berkeley

Prof. Vince Voelzs lab has published an exciting paper on their recent successes with predicting the structures of protein-like molecules called peptoids (here). Peptoids are similar to proteins but with a rearrangement in their chemistry (see example below). Their similarity to proteins allows peptoids to function like proteins.


Full Article here
New FAH client and video
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,814,000
Work Units: 6,597

Posted: Sun Feb 24, 2013 04:02 pm
It looks like it's been a pretty busy month for Stanford, they released a new client and video.

Quote:
We've rolled out the latest version 7.3 client to the main web site. This new client should be much easier to install and comes with a new web interface which is simpler and easier to use.


Full article here

DNA- Repairing Protein May Be Key To Preventing Recurrence Of Some Cancers
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,814,000
Work Units: 6,597

Posted: Thu Jan 31, 2013 01:57 am
Quote:
Just as the body can become resistant to antibiotics, certain methods of killing cancer tumors can end up creating resistant tumor cells. But a University of Central Florida professor has found a protein present in several types of cancer, including breast and ovarian cancer, which could be helpful in preventing tumors from coming back.

The protein, KLF8, appears to protect tumor cells from drugs aimed at killing them and even aid the tumor cells ability to regenerate.



Full Article here
New FAH GPU programmer Yutong Zhao
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,814,000
Work Units: 6,597

Posted: Sat Dec 29, 2012 02:02 am
Well we're still here, yet another doomsday avoided.

It has been a rather slow month for news. Stanford hired a new F@H GPU programmer.

Quote:
We have had an unfilled spot in our GPU programming team for a few months and I'm happy to announce that we recently made a great new hire: Yutong Zhao.

Yutong completed his undergraduate degree in Math, Chemistry, and Biochemistry from the University of Toronto, and a Masters degree in Computational Chemistry from HKUST, focusing on GPU-powered clustering algorithms.


Full Article: here




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