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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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 Boingo04/17/14 
 DanielGordon04/16/14 
 Huberthans04/15/14 
 Voxelot04/11/14 
Isolating immune cells to study how they ward off oral diseases
Refined categorization may improve prediction of patient survival in RECIST 1.1
Blocking protein partnership has implications for cancer treatment
Ovarian cancer patients may benefit from nanoparticles designed to deliver three cancer drugs at a time
Gene variant makes eaters of processed meat 'more likely to get colorectal cancer'
Teens who conform to gender norms 'more likely to engage in cancer-risk behaviors'
Severe sleep apnea linked to increased risk of stroke, cancer and death
Processing can affect size of nanocarriers for targeted drug delivery
Research shows processing can affect size of nano carriers for targeted drug delivery
Study suggests gene panels as a useful, cheaper alternative to whole-genome sequencing
New blood test 'accurately predicts breast cancer recurrence'
New state-of-the-art educational platform for uro-onco professionals now online
Breakthrough technology to enable doctors to select more effective treatment for cancer patients on a personalised basis
Hepatocellular carcinoma: new advances in diagnosis, staging and treatment all predicted to improve patient outcomes
How and when nerve and brain cells are formed could open doors to targeted cancer therapies
Genetic evidence supports role virus-fighting genes in cancer development
New strategies suggested for kidney regeneration by gene linked to Wilms tumors, a pediatric kidney cancer
ZMYND11 'reads' methylated variant to thwart cancer; tied to breast cancer patient survival
Too much of a protein called c-FLIPR can trigger autoimmune diseases
Tough liver cancer may be treated with immunotherapy
Discovery of latent bioluminescence in fruit flies holds promise for expanded use of bioluminescence imaging tools
3D-printed kidneys could become standard for simulated cancer surgery
Chemotherapy before or after surgery for high-risk bladder cancer improves survival, but is not routinely administered
Virus-fighting genes linked to mutations in cancer: Genetic evidence supports role of gene family in cancer development
Genetic changes associated with epigenetic changes increase risk of developing cancer
Apathy in older adults linked to increased brain shrinkage
Modified stem cells may offer way to treat Alzheimer's disease
Gene variant gives women higher risk for Alzheimer's
Alzheimer's disease research could be revolutionized by new mouse model
Could Silly Putty help treat neurological disorders?
Researchers at the University of Valencia discover new molecules against Alzheimer's disease
Improving cognition later in life through physical activity
Innovative, coordinated brain care could save billions of health care dollars
Why is there an inverse association between cancer and Alzheimer's?
New dementia care models to improve care for older adults with Alzheimer's disease
Working memory boosted by green tea
Caring for grandkids once a week keeps grandmas sharp
Presymptomatic diagnosis of Alzheimer's disease will alter life with a 'brain at risk'
Likely connection between white matter and cognitive health
2 new studies find no evidence of Alzheimer's disease-associated changes in adolescents carrying genetic risk factors
African Americans may be at a greatly increased risk for Alzheimer's disease
Complex relationship between slow-wave sleep and odor memory revealed
Green tea may boost our working memory
Scientists discover big clue to how caffeine wards off Alzheimer's
No evidence of Alzheimer's Disease-associated changes in adolescents carrying genetic risk factors
Breakthrough may revolutionize the study of modern-day enzymes
The origin of Lou Gehrig's disease may have just been discovered
How zinc regulates a key enzyme involved in cell death
Dog watch - How attention changes in the course of a dog's life
'Sewing machine' idea gives insight into origins of Alzheimer's
Key 'sperm meets egg' protein discovery holds promise for fertility treatments
Research shows processing can affect size of nano carriers for targeted drug delivery
Study on Mt. Everest shows how people get type 2 diabetes
Virus-fighting genes linked to mutations in cancer: Genetic evidence supports role of gene family in cancer development
Researchers at the University of Valencia discover new molecules against Alzheimer's disease
Key to stronger, more effective antibiotics could be enzyme 'wrench'
New target in flu virus may open route to better drugs
Obsessive-compulsive disorder may reflect a propensity for bad habits
Team solves decades-old mystery of how cells keep from bursting
Researchers demonstrates advantages of the HOPE fixation strategy
How does the 'kissing disease' replicate itself?
Identification of <em>pelo</em>, a host gene needed for efficient virus production
New agents may revitalize antibiotics to fight superbugs
Higher blood pressure is linked to a lower tendency to worry
Method offers potential for understanding anti-bacterial resistance
Scientists discover key cells involved in touch sensation
The hormone that allows us to love may also encourage us to lie
The origin of Lou Gehrig's disease may have just been discovered
Scientists identify protein that spurs spread of colon cancer
Team identifies novel biomarker for head and neck cancer and non-small cell lung cancer
Cell metabolism discovery could spawn treatments for cancer or common cold
Cells measure surface area to know when to divide
Time, trust and transparency keys to minority biospecimen collection
The acrobatic motor protein Kif15 could pave the way for new cancer therapies
Plasma tool for destroying cancer cells
  • Stickies: 0
  • News Articles: 153
  • Pages: 31
New FAH GPU programmer Yutong Zhao
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,736,559
Work Units: 6,433

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




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


Posts: 98
Points: 2,736,559
Work Units: 6,433

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

Quote:
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 (https://simtk.org/home/openmm).



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


Posts: 98
Points: 2,736,559
Work Units: 6,433

Posted: Sun Oct 28, 2012 04:04 am
Quote:
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

Quote:
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=http://folding.typepad.com/news/2012/10/unified-gpusmp-benchmarking-scheme-equal-points-for-equal-work.html[/url]
New Gromacs, new you.
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,736,559
Work Units: 6,433

Posted: Thu Sep 27, 2012 07:16 am
Quote:
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

Quote:
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.
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,736,559
Work Units: 6,433

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

Quote:
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




Quote:
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
  • Stickies: 0
  • News Articles: 153
  • Pages: 31
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