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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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DNA in 'gene deserts' linked with breast cancer
Study strengthens evidence that breastfeeding can help prevent aggressive breast cancer in African-Americans
Canine lymphoma: new hope for beloved family pets
Identifying molecules that increase risks of cancer using graphene sensor
Powerful new weapon to battle superbugs
New therapy approach for breast cancer suggested by how cancer cells adapt energy needs to spread to other organs
Experimental therapy stopped the metastasis of breast and ovarian cancers in lab mice
Freeing the immune system to destroy cancer
Palliative care not available for many patients with terminal cancer
New cancer drug target involving lipid chemical messengers
E-cigarettes 'not helping cancer patients to quit smoking'
Curcumin, special peptides boost cancer-blocking PIAS3 to neutralize cancer-activating STAT3 in mesothelioma
Adding chemotherapy to radiation treatment not effective in treating vulvar cancer, UPMC study shows
Imaging of metastatic cancer may be revolutionized by new non-invasive technique
Mapping complex trait genes in multiparental populations
The eyes of flies reveal abnormal properties of cancer protein
Researchers shed light on how breast implants may cause rare lymphoma
Neck surgery unnecessary for many throat cancer patients
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
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
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'
Patients with advanced dementia continue receiving medications of questionable benefit
Apolipoprotein E and apolipoprotein CI are involved in cognitive impairment progression in Chinese late-onset Alzheimer's disease
Researchers track harmful immune reactions in the brain, suggest reason why HIV patients develop dementia
Association between diabetes mellitus, mild cognitive impairment and being middle aged and older
Memory and Alzheimer's disease
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'
Important regulators of immune cell response identified
Movable cytoskeleton membrane fabricated for first time
Genetic link identified between the circadian clock and seasonal timing
Body clock link could aid obesity treatments
Are females more susceptible to effects of marijuana?
Corals could provide a general model for understanding ciliary processes related to mass transport and disease
A call to investigators to study mysterious cloud-like collections in cells
Are molecular mechanisms to blame for how stress affects us?
New type of cell movement discovered
Research reveals mechanism behind cell protein remodeling within a family of cancers
Artificial virus improves delivery of new generations of pharmaceuticals
Stem cell breakthrough for 'Cinderella cells'
Neanderthals and modern humans co-existed for thousands of years
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New FAH GPU programmer Yutong Zhao
[H]ard|Folding Administrator

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

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.

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

Update on on-going software development in FAH
[H]ard|Folding Administrator

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

Posted: Tue Nov 27, 2012 09:14 pm
Stanford posted an update on the next client and core releases.

We have several on-going software development efforts and I'd like to give donors an update.

v7 client. Joe Coffland and his team have been working hard on new client releases. 7.2.9 has just been released and a new version will be undergoing beta testing soon. Moreover, we are continuing work on improving the v7 client for windows and squashing the remaining bugs. Moreover, there's additional effort in OSX due to the hiring of a programmer (Kevin Bernhagen) just for the OSX client, as well as additional work for smoother OSX and linux installs.

Gromacs core. The Gromacs core team (Prof. Michael Shirts and Prof. Peter Kasson and their labs, at the University of Virginia) are working on the new cores based on the new version of gromacs (4.6).

New OpenMM core. The OpenMM team at Stanford (Dr. Peter Eastman and Yutong Zhao) are working on speed improvements for OpenMM (the basis of the FAH GPU core) in general, but in particular optimizations for Kepler and AMD (in coordination with engineers at NVIDIA and AMD, respectively). Yutong has a new FAH GPU core working in the lab and we are doing internal testing on it. Since openMM is full open source, you can see more details, including a commit and change log, at the openMM web site (

Full Article here
Life with Playstation ending, FAH team continuing to look to push the envelope.
[H]ard|Folding Administrator

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

Posted: Sun Oct 28, 2012 04:04 am
For several years, we have worked closely with Sony to bring Folding@home to the PS3. We're excited about what we've been able to do. Since the PS3 started folding in 2007, we've done some really amazing things, with several announcements this year acknowledging advancements.

Full Article here.

Unified GPU/SMP benchmarking scheme: equal points for equal work

The current benchmarking calculations for SMP and GPU projects are performed on different machines since originally the SMP cores could not perform the calculations that the GPUs cores could and vice versa (GPUs were only for implicit solvent calculations and SMP only for explicit solvent calculations). With recent advances in both cores and completion of our testing of these capabilities to ensure agreement, we are now confident we can do the same work on both cores. Thus, we feel that it is time to unify GPU and SMP benchmarking, both for simplicity and fairness.

Full Article [url=[/url]
New Gromacs, new you.
[H]ard|Folding Administrator

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

Posted: Thu Sep 27, 2012 07:16 am
A new version of Gromacs (4.6) is coming, and were working to bring it to Folding@home. The new code contains a number of improvements (more than youd expect for a minor version number!), and well post about some of the individual features as we go. Not all of them will be available on F@h immediately, as some will require substantial development work over the next few months. But some of the basics are new free energy methods from our very own Prof. Michael Shirts, new and slightly faster inner-loop code, and some important tweaks to parallelization. Free energy calculations allow us to calculate things like how tightly drugs bind to proteins and the strength of attraction between protein components when pulled apart. And you, of course, know what faster inner-loop code and better parallelization mean!

Full Article: here

New methods for analyzing FAH data

Two general objectives of the Folding@home project are (1) to explain the molecular origins of existing experimental data and (2) to provide new insights that will inspire the next generation of cutting edge experiments. We have made tremendous progress in both areas, but particularly in the first area. Obtaining new insight is even more of an art and, therefore, less automatable.

To help facilitate new insights, I recently developed a Bayesian algorithm for coarse-graining our models. To explain, when we are studying some processlike the folding of a particular proteinwe typically start by drawing on the computing resources you share with us to run extensive simulations of the process. Next, we build a Markov model from this data. As Ive explained previously, these models are something like maps of the conformational space a protein explores. Specifically, they enumerate conformations the protein can adopt, how likely the protein is to form each of these structures, and how long it takes to morph from one structure to another. Typically, our initial models have tens of thousands of parameters and are capable of capturing fine details of the process at hand. Such models are superb for making a connection with experiments because we can capture all the little details that contribute to particular experimental observations. However, they are extremely hard to understand. Therefore, it is to our advantage to coarse-grain them. That is, we attempt to build a model with very few parameters that is as close as possible to the original, complicated model. If done properly, the new model can capture the essence of the phenomenon in a way that is easier for us to wrap our minds around. Based on the understanding this new model provides, we can start to generate new hypotheses and then test them with our more complicated models and, ultimately, via experiment.

Full Article: here
New way to diagnose locations of diseases.
[H]ard|Folding Administrator

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

Posted: Thu Aug 30, 2012 02:38 am
Not much news out of Stanford this month, but I did find a couple interesting articles.

New Ultraviolet Light Can Pinpoint Location Of Diseases

A new study published in the Online Early Edition of Proceedings of the National Academy of Sciences reveals that Johns Hopkins researchers have developed a synthetic protein, which, when activated under ultraviolet lighting, can show doctors exactly where certain medical disorders are located, such as arthritis and cancer.

Full Article here

New Computer Simulation Models Metastasis

Cancer metastasis, the escape and spread of primary tumor cells, is a common cause of cancer-related deaths. But metastasis remains poorly understood. Studies indicate that when a primary tumor breaks through a blood vessel wall, blood's "stickiness" tears off tumor cells the way a piece of tape tears wrapping paper. Until now, no one knew the physical forces involved in this process, the first step in metastasis. Using a statistical technique employed by animators, scientists created a new computer simulation that reveals how cancer cells enter the bloodstream. The researchers present their work in a paper accepted to the American Institute of Physics (AIP) journal Physics of Fluids.

Full Article here
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  • News Articles: 158
  • Pages: 32
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