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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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 M._Daniel09/20/14 
 Brian_Northcutt09/15/14 
 chinoquezada09/14/14 
Researchers shed light on how breast implants may cause rare lymphoma
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For recurrent head and neck cancers a combination of targeted radiation and drug therapy is less toxic
Exercise can enhance tumor-shrinking effects of chemotherapy
More accurate treatment, greater patient comfort provided by new radiosurgery technology
Preserved mobility in malignant spinal cord compression
Cancer resistance may one day be treated with epigenetic drugs
New molecule 'allows umbilical cord stem cells to multiply'
Global team finds new genetic variants that raise risk of prostate cancer
Master regulator of cells' heat shock response identified
Rutgers Cancer Institute of New Jersey studying low participation in cancer screenings by South Asian population
Cell surface sugars can promote or inhibit cancer depending upon stage
A single protein can mean the difference between life-long chronic infection or cure for hepatitis
Potential for targeted treatments with new knowledge of genes driving bladder cancer
Final pieces to the circadian clock puzzle found
Specific baldness pattern linked with increased prostate cancer risk
American Association for Cancer Research releases 2014 cancer progress report: research is transforming lives
Cancer Council publishes first Australian guidelines on Barrett's Oesophagus and oesophageal adenocarcinoma
Research sheds light on cognitive losses seen with chemotherapy, autoimmune diseases
Study indicates that learning and memory defects are reversible in zebrafish model of neurofibromatosis, a human genetic disease
Detecting disease by the shadow it casts
Patient profiling may lead to earlier transition from active treatment to hospice care
New cellular connection makes scientific history
Breast cancer screening in over-70s 'may lead to overdiagnosis'
Patients with head and neck cancers resistant to cetuximab may benefit from an investigational drug
UB researchers corroborate the neuroprotective effects of Sirtuin 1 activation on mice with Alzheimer's disease
Concussion-related brain disease identified in living brain
Sedentary behavior 'may counteract brain benefits of exercise in older adults'
Dementia risk reduction through tobacco control and better prevention, detection and control of hypertension and diabetes
Measuring modified protein structures
The cell recognizes the buildup of misfolded proteins, offers insight into Alzheimer's, ALS, Huntington's, Parkinson's, and type 2 diabetes
Brain may 'work around' early Alzheimer's damage
The young brains of city dwellers harmed by air pollution
Discovery may lead to improved memory, cognitive function in Alzheimer's patients
In mouse model of Alzheimer's disease, targeted immune booster removes toxic proteins
sPIF protects against neuronal death and brain injury
Memory loss more common in people with blood type AB
Poor recording of physical health and medication could be causing dementia trials to fail
Neurodegenerative diseases can be caused by broken signals
Increased Alzheimer's risk linked to long-term benzodiazepine use
Gene 'may slow aging of entire body when activated in key organs'
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Apolipoprotein E and apolipoprotein CI are involved in cognitive impairment progression in Chinese late-onset Alzheimer's disease
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Association between diabetes mellitus, mild cognitive impairment and being middle aged and older
Memory and Alzheimer's disease
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Pilot study of socially-assistive robots that help children with autism to learn imitative behavior
Late and early onset Alzheimer's affect brain function in similar way
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Pupil size shows reliability of decisions
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Gene 'may slow aging of entire body when activated in key organs'
Important regulators of immune cell response identified
Movable cytoskeleton membrane fabricated for first time
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New type of cell movement discovered
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MRC publishes a review of the UK molecular pathology landscape
One of the biggest challenges for single-cell research is picking out only one cell from a collection of millions - problem solved
  • Stickies: 0
  • News Articles: 158
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Core 17 update
King_N
[H]ard|Folding Administrator


Posts: 103
Points: 2,857,126
Work Units: 6,701

Posted: Wed May 29, 2013 03:34 am
F@H GPU developer gives us a detailed video update of the new core 17 features.

Quote:
Some of the key highlights are:
-Up to 120,000 PPD on GTX Titan, and 110,000 PPD on HD 7970
-Support for more diverse simulations
-Linux support on NVIDIA cards and 64bit OSes
-FAHBench updated to use the latest OpenMM and display version information




Full article and video here
Potential Therapy For Alzheimer's
King_N
[H]ard|Folding Administrator


Posts: 103
Points: 2,857,126
Work Units: 6,701

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: 103
Points: 2,857,126
Work Units: 6,701

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: 103
Points: 2,857,126
Work Units: 6,701

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: 103
Points: 2,857,126
Work Units: 6,701

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
  • Stickies: 0
  • News Articles: 158
  • Pages: 32
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