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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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Metastasis more likely to occur with clusters of circulating tumor cells rather than single cells
New type of cell movement discovered
Research reveals mechanism behind cell protein remodeling within a family of cancers
How high-fat diets promote intestinal cancer
How premalignant cells can sense oncogenesis and halt growth
Exploiting a common cancer defense shows promise as a new cancer therapy
Targeted therapy for hepatocellular carcinoma using nanotechnology and the thunder god vine
New ESC registries launched on cardiac oncology and ACS
Leading scientists call for a stop to non-essential use of fluorochemicals
Versatile multi-tasking nanoparticles offer a wide variety of diagnostic and therapeutic applications
Acoustic device that separates tumor cells from blood cells could help assess cancer's spread
Sound waves separate tumor and blood cells
Probing cancer's molecular make-up
New approach to treating cancer: personalized radiation therapy during - instead of after - cancer surgery
Knowledge is power: UCLA study finds men who are uneducated about their prostate cancer have difficulty making good treatment choices
Gentle separation of cells using tilted acoustic tweezers
The epigenetic signature could be key to glioblastoma's therapeutic resistance
Potential for early attack on malaria offered by cancer-fighting drugs
Depression untreated in many cancer patients, new approach could help
Discovery of navigation system used by cancer, nerve cells
New approach developed to identify 'drivers' of cancer
Cutting the liver piece by piece gives hope to patients with cancer that has spread from the intestine
Leukemia and other cancers could be treated more effectively with drug used for DNA repair defects
Study shows a direct correlation between smoking and mortality
Insights into the cancer epigenome have implications for treatment, prevention
Late and early onset Alzheimer's affect brain function in similar way
Memory boosted by electric current to brain: finding has implications for stroke, Alzheimer's and brain injury
Marijuana compound shows promise for treating Alzheimer's disease in preclinical study
Unprecedented detail of intact neuronal receptor should serve as template and guide for the design of therapeutic compounds
Mindfulness training can improve quality of life for memory impaired and their caregivers
Weight loss following bariatric surgery leads to improved brain function, could reduce risk of Alzheimer's in obese people
APOE, diagnostic accuracy of CSF biomarkers for Alzheimer disease
Missing protein associated with early signs of dementia
Research underway to create pomegranate drug to stem Alzheimer's and Parkinson's
Cognitive impairment increases risk of stroke
Retinal thinning can be used as an early marker for frontotemporal dementia, prior to the onset of cognitive symptoms
Cognitive impairment 'associated with a higher risk of stroke'
New mouse line offers new insights for treatments of epilepsy, Alzheimer's
Alzheimer's disease: rAAV/ABAD-DP-6His attenuates oxidative stress induced injury of PC12 cells
Dementia risk increased for obese people in 30s, but reduced for obese seniors
Pulse pressure and elasticity of arteries in the brain mapped for arterial health and aging
Alzheimer's disease: are we close to finding a cure?
Zebrafish help to unravel Alzheimer's disease
Atypical antipsychotic drug use increases risk for acute kidney injury
Examining the brain's chromosomal make-up in relation to Alzheimer's disease
DNA methylation in brain 'linked to Alzheimer's disease'
Researchers find RNA-targeted drug candidate for Lou Gehrig's disease
Understanding of Alzheimer's disease improved by epigenetic breakthrough
Jet lag controlled by a single gene
Protein implicated in Alzheimer's disease has important treatment potential in genetic form of epilepsy
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
Scientists grow fully functional thymus in mice from scratch
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
Treating pain by blocking the 'chili-pepper receptor'
Slippery material for lubricating joints inspired by nature
Scripps research institute chemists uncover powerful new click chemistry reactivity
Parasitic worms sniff out their victims as "cruisers" or "ambushers"
Scientists build first functional 3D brain tissue model
"Dimmer switch" drug idea could tackle schizophrenia
Cell signaling pathway linked to obesity and Type 2 diabetes
Probes that repair genes inspired by butterfly proboscis
The speed of a signal seals the fate of an embryonic cell
Scientists reproduce evolutionary changes by manipulating embryonic development of mice
New insights into why adolescents carry meningitis-causing bacteria
Self-assembling anti-cancer molecules created in minutes, like a self-assembling 'Lego Death Star'
Softening of human features 'coincided with technological breakthrough'
Chemists create nanofibers using unprecedented new method
Wound closure involves cooperative compression
Biomedical discoveries accelerated by see-through organs and bodies
Advances in maritime anti-fouling and biomedicine provided by barnacle cyprid adhesives
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New FAH GPU programmer Yutong Zhao
[H]ard|Folding Administrator

Posts: 103
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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: 2,847,566
Work Units: 6,669

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: 2,847,566
Work Units: 6,669

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: 2,847,566
Work Units: 6,669

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: 2,847,566
Work Units: 6,669

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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