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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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Breast cancer: are men the forgotten victims?
Thyroid cancer: additional new subgroup analyses for Phase III SELECT trial
Immunotherapy could stop resistance to radiotherapy
Study: tumor BRACAnalysis CDx identifies 44 percent more candidates for PARP therapy
New imaging technique could revolutionise how children with neuroblastoma are diagnosed and treated
Targeted treatment could halt womb cancer growth
Study defines an interaction between key proteins in cell division
Making diagnostic medical imaging safer
Medicare law aimed a reducing chemotherapy cost turned out to have little impact
Discovery of shining cells responsible for developing tumors
Study examines medical professional liability claims related to esophageal cancer screening
Many patients lack information about the use of targeted therapies, oncologists say
Significant presence of women in oncology, but still under-representation in leadership positions, Greek survey shows
What are the top 10 leading causes of death in the US?
Potent new cancer drugs likely with new protein 'map'
Survey reveals emotional exhaustion affects many cancer specialists
New estrogen-related breast cancer mechanism detected
Cancer during pregnancy: chemotherapy and radiotherapy are safe for babies, studies show
Anamorelin shown to improve appetite and body mass in patients with cancer anorexia-cachexia
Second-line afatinib significantly improves progression-free survival in recurrent or metastatic head and neck cancer, phase III trial shows
Rolapitant reduces nausea and vomiting in phase III trial
Strategy to reduce side effects in modern cancer therapy
Taller people at reduced risk of esophageal cancer
Genetic 'instruction set' for antibodies knocks down hepatitis C in mice
Scientists shed light on how to block protein that causes cancer, Alzheimer's
Hope of a treatment for deadly genetic disease, MPS IIIB
Protein that causes frontotemporal dementia also implicated in Alzheimer's disease
Remote healthcare for an aging population
Promising Alzheimer's treatment being tested by NeuroEM Therapeutics
Scientists shed light on how to block protein that causes cancer, Alzheimer's
Regeneration of brain stem cells boosted by turmeric compound
The emotion lingers long after the memories have vanished in Alzheimer's patients
Promising drug candidate for Alzheimer's found in turmeric compound
Viewing drugs' effect on living brain now possible with first mouse model for ALS dementia
New 'designer proteins' created in fight against Alzheimer's and cancer
Online resource encourages everyone to improve brain health
Memory complaints could be early indicator of future dementia risk
UK-based chemists report 'designer proteins' breakthrough
Cognitively demanding visual motor task can identify those at high risk for Alzheimer's disease
Down syndrome helps researchers understand Alzheimer's disease
Impaired brain signaling pathway 'may be a cause of Alzheimer's'
World Alzheimer Report 2014: the key points
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
Study shows how chimpanzees share skills
Antibiotic exposure associated with early childhood obesity
Customising chemotherapy in lung cancer
Malaria severity influenced by five human genes, say researchers
Scientists shed light on how to block protein that causes cancer, Alzheimer's
Newly discovered marker may lead to early detection of pancreatic cancer
Research uncovers tumors self-protection mechanism
Magnetic field opens and closes nanovesicle
Protein controlling gut's protective force field identified: Immune-system receptor encourages growth of bacterial shield during illness
More evidence that Neanderthals and modern humans overlapped
Diabetes study: investigating fluctuations in blood sugar
Western University researchers explain the highs and lows of marijuana use
UK-based chemists report 'designer proteins' breakthrough
An old drug yields a potential new class of antibiotics
Mechanism of Parkinson's spread demonstrated
Healthy humans 'harbor an average of five viruses'
Pupil size shows reliability of decisions
Endocrine-related protein found to be master regulator in other important diseases
How do I smell? Much the same as how you see
Ebola virus protein offers potential drug target
Glaucoma cure may lie in targeting 'stiff cells' that impede fluid drainage
Is the pattern of brain folding a "fingerprint" for schizophrenia?
Scientists reset human stem cells in 'significant milestone' in medicine
Deactivating a cell protein may halt progress of rheumatoid arthritis
Gene 'may slow aging of entire body when activated in key organs'
  • Stickies: 0
  • News Articles: 159
  • Pages: 32
Computerized Brain-Fitness Program Improves Memory Of Older Adults
King_N
[H]ard|Folding Administrator


Posts: 104
Points: 2,859,398
Work Units: 6,705

Posted: Fri Jun 28, 2013 03:30 am
Quote:
UCLA researchers have found that older adults who regularly used a brain-fitness program on a computer demonstrated significantly improved memory and language skills.



Full Article: here



Robo-Pets May Contribute to Quality of Life for Those With Dementia

Quote:
A study has found that interacting with a therapeutic robot companion made people with mid- to late-stage dementia less anxious and also had a positive influence on their quality of life.



Full Article: here



Protein Identified That Contributes To Cognitive Decline In Alzheimer's Disease

Quote:
Researchers at Columbia University Medical Center (CUMC) have demonstrated that a protein called caspase-2 is a key regulator of a signaling pathway that leads to cognitive decline in Alzheimer's disease. The findings, made in a mouse model of Alzheimer's, suggest that inhibiting this protein could prevent the neuronal damage and subsequent cognitive decline associated with the disease. The study was published this month in the online journal Nature Communications.



Full Article: here
Core 17 update
King_N
[H]ard|Folding Administrator


Posts: 104
Points: 2,859,398
Work Units: 6,705

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: 104
Points: 2,859,398
Work Units: 6,705

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: 104
Points: 2,859,398
Work Units: 6,705

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: 104
Points: 2,859,398
Work Units: 6,705

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

  • Stickies: 0
  • News Articles: 159
  • Pages: 32
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