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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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Surgery associated with better survival for patients with advanced laryngeal cancer
Genetics and lifestyle have a strong impact on biomarkers for inflammation and cancer
NSAIDs may halve breast cancer recurrence in overweight women
Blueprint for the next generation of chronic myeloid leukemia treatment
NICE clears path for patient access to Revlimid® (lenalidomide) for rare form of blood cancer
Blood test may revolutionize brain cancer diagnosis
Web-based app developed to predict glioma mutations
Transient axonal glycoprotein-1 induces apoptosis-related gene expression without triggering glioma apoptosis
Dasatinib, a leukemia drug, has the potential to treat many cancers
Gastric cancer: could Botox be an alternative to chemo?
Turkish man pleads guilty to importing illegal cancer drugs
Microfluidic device monitors key step in development of tumor metastases
Myc inhibition is an effective therapeutic strategy against the most aggressive of all brain tumors
Mechanism identified that halts progression of abnormal cells into cancer
In an ecosystem within us, microbes evolved to sway food choices
How tumor cells transition to invasion revealed by microchip
An enzyme therapy may prevent skeletal abnormalities associated with the genetic disorder neurofibromatosis type-1
New ways to treat solid tumours
Older patients with limited life expectancy still receiving cancer screenings
Tumors shrink following bacteria injection
Benefits of vitamin A cancer therapy blocked by a protein
Preventing transplant rejection using stimuli-responsive drug delivery system
C. noyvi-NT shrinks tumors when injected into rats, dogs and humans
For kidney cancer patients, less radical procedures offer similar cancer control compared to surgery
Childhood cancer survivors do not adhere to American Cancer Society's guidelines on healthy living
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
Decreased brain activity in Alzheimer's disease leads to decline in daily functioning
Yizhijiannao granules inhibit neuronal apoptosis in Alzheimer's disease
New small molecules target mutation in ALS and a form of dementia
Cognitive decline in older adults may be reduced by digital literacy
Study demonstrates key brain region in contextual memories
New target for treatment of neuronal injury in the hippocampus of rats with vascular dementia
In PC12 cell apoptosis, the role of Notch-1 signaling pathway is induced by amyloid beta-peptide (25-35)
Normal cognition in patient without apolipoprotein E, risk factor for Alzheimer
Some areas of the brain 'may not slow down with aging'
Mild cognitive impairment quadruples risk of dementia
Cognitive decline may increase the risk of stroke
Link found between dementia and vitamin D deficiency
How spiders spin silk has implications for Alzheimer's disease
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
Mouse sperm form cooperative groups
See-through mice may improve diagnosis, treatment of human illness
Video explains why dogs smell each other's behinds
Cancer cells allowed to divide even when oxygen-starved by cell's recycling center
"Killer sperm" prevents mating between worm species
One third of cancer patients are killed by a 'fat-burning' process termed cachexia related to obesity, CNIO researchers say
  • Stickies: 0
  • News Articles: 157
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Client Version 7(Beta)
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,838,675
Work Units: 6,652

Posted: Tue Mar 29, 2011 08:41 pm
Stanford just released a new beta client for version 7.

Quote:
I am happy to announce that after many months of development and testing the new version 7 Folding@home client software is now available for open-beta testing. The V7 client is a complete rewrite of the previous client for Windows, OS-X and Linux with the following goals:

1.To make the installation and startup user-friendly for the novice.
2.To integrate the user interface into a single Monitor/Control program that manages the functionality previously contained in separate clients.
3.To create a forward-looking design that can be readily expanded to incorporate new Folding Cores without the need to issue new client releases.
4.To greatly improve previously problematic aspects including support for SMP, GPU, and the 3D viewer.


Download Available here.
New SMP clients available.
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,838,675
Work Units: 6,652

Posted: Mon Feb 28, 2011 07:56 am
Stanford just released the new 6.34 SMP clients.

Download Available here



New Client Released
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,838,675
Work Units: 6,652

Posted: Sat Jan 29, 2011 10:44 am
Stanford just released GPU3 client version 641.

Quote:
The changes to this version of the client include the addition of a -forcegpu flag ='nvidia_g80_1.0' ; this flag will signal a compute capability of 1.0 (GPU species=10); if the flag ''nvidia_g80' is used the compute capability will be reported as 1.1 (GPU species=11). Also a pop-up dialog box now appears reporting an error, if the -forcegpu flag is unrecognized; the client then exits.


Download Available here



Everything back to normal
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,838,675
Work Units: 6,652

Posted: Fri Dec 31, 2010 03:44 am
Stanford appears to have compleated thier server maintenance, the maintenance they ran did cause a few glitches on this end however everything appears to be back to normal once again.

Have a Happy New Year everyone.
2 new research articles released
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,838,675
Work Units: 6,652

Posted: Sat Nov 27, 2010 03:39 pm
Stanford has released 2 new research articles.

Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins

Quote:
Multiple variants of the AMBER all-atom force field were quantitatively evaluated with respect to their ability to accurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A21 and Fs helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100 ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SB force field showed significant helix-destabilizing tendencies, with beta bridge formation occurring in helical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, while showing adequate helical propensities for both peptides and stabilizing apolipophorin-III, (i) predicts an unexpected decrease in helicity with ALA to ARG+ substitution, (ii) lacks experimentally observed 3-10 helical content, and (iii) deviates strongly from average apolipophorin-III NMR structural properties. As is observed for AMBER-99SB, AMBER-03 significantly overweighs the contribution of extended and polyproline backbone configurations to the conformational equilibrium. In contrast, the AMBER-99phi force field, which was previously shown to best reproduce experimental measurements of the helix-coil transition in model helical peptides, adequately stabilizes apolipophorin-III and yields both an average gyration radius and polar solvent exposed surface area that are in excellent agreement with the NMR ensemble.


Full article here


Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

Quote:
Conformational equilibrium within the ubiquitous GNRA tetraloop motif was simulated at the ensemble level, including 10,000 independent all atom molecular dynamics trajectories totaling over 110 microseconds of simulation time. This robust sampling reveals a highly dynamic structure comprised of 15 conformational microstates. We assemble a Markov model that includes transitions ranging from the nanosecond to microsecond timescales and is dominated by six key loop conformations that contribute to fluctuations around the native state. Mining of the Protein Data Bank provides an abundance of structures in which GNRA tetraloops participate in tertiary contact formation. Most predominantly observed in the experimental data are interactions of the native loop structure within the minor groove of adjacent helical regions. Additionally, a second trend is observed in which the tetraloop assumes non-native conformations while participating in multiple tertiary contacts, in some cases involving multiple possible loop conformations. This tetraloop flexibility can act to counterbalance the energetic penalty associated with assuming non-native loop structures in forming tertiary contacts. The GNRA motif has thus evolved not only to readily participate in simple tertiary interactions involving native loop structure, but also to easily adapt tetraloop secondary conformation in order to participate in larger, more complex tertiary interactions.


Full article here

  • Stickies: 0
  • News Articles: 157
  • Pages: 32
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