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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.



How to Join | Project Faqs | Project Add-ons | Statistics | Download Client
New Members
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 PatrickCalender44007/22/14 
 Rallor07/21/14 
 Jasjar07/20/14 
 shoerider07/17/14 
Scientists discover gene that stops spread of deadly lung cancer
Genes identified that contribute to radiation resistance
Intervention strategy in in low-income families helps parents nurture children and reduce inflammation
Novel regulator of the activity of a protein inactive in over 50% of human tumors
Enzyme lost in 100 percent of kidney tumors analyzed
New, powerful single-cell technique developed to study environmental effects on DNA
In diseases like cancers and psoriasis, degradation is key to the activity of the miR-21 oncomiR
'Pathogenic connection' between cancer and autoimmune disorders
Innovative data collection system for cancer patients developed to improve care and outcomes
Hidden information behind imaging tests for cancer may unlock new approaches to radiation therapy
Study examines presence of uterine cancers among women at the time of hysterectomy using morcellation
Targeted virus could boost chemo's effects for arm and leg cancer
Enzyme may halt tumor growth in kidney cancer
First study worldwide to show higher concentration of trace elements in bone cancer
Patients with advanced cancer can benefit from programs combining exercise and nutritional advice
Gene discovered that links stem cells, aging and cancer
Mapping decade of discovery to potential anticancer agent
Technique to draw molecules from live cells using magnetic nanomaterials offers promise for cancer diagnosis, gene therapy
Rare form of tongue cancer suggests screening vigilance
The browning of white fat may be at the root of cancer-related wasting syndrome
Researching cancer's 'footprint' on our evolution
Structure of protein vital to cancer development is mapped
Bexarotene's effect on Alzheimer's may depend on severity of disease
Naloxegol being tested to counteract constipation caused by opioid painkillers
Could cat feces help cure cancer?
Are life expectancy increases among older Americans slowing?
Enzyme linked to Alzheimer's disease
Social contact, peer support and self-help can positively benefit people with dementia
Human neurodegenerative diseases may be impacted by discovery of a new cellular garbage control pathway
Two-way interaction between neurons and astrocytes plays an important role in the processes of learning and memory
New studies presented at Alzheimer's Association International conference demonstrate diagnostic value of [<sup>18</sup>F]flutemetamol
Neuronal edema in Alzheimer's disease rats reduced by acupuncture and moxibustion
Bexarotene's effect on Alzheimer's may depend on severity of disease
Potential cause of preeclampsia may share links with disorders such as Alzheimer's
Can fish oil protect against brain damage caused by alcohol abuse?
Age-related changes in lateral ventricular width and periventricular white matter by diffusion tensor imaging
Older adults benefit from fish oil supplements which reduce incidence of cognitive decline, may improve memory function
Researchers seeking to smuggle pharmacological agents across the blood-brain barrier
Alzheimer's Association International Conference 2014 selected highlights
Gardens could benefit dementia patients and their carers
Signaling pathway for ginsenoside Rb1 promoting hippocampal neuronal neurite outgrowth
Alzheimer's disease not prevented by B vitamins
Genetic variant conveys significant protection against Alzheimer's disease
Memory and learning deficits restored in Alzheimer's mouse models
ANAVEX 3-71 highly effective and disease-modifying against all major Alzheimer's hallmarks in preclinical disease model
New data on possible protective behaviors and dementia risk factors emerges at Alzheimer's Association International Conference 2014
Could eye and smell tests offer early Alzheimer's diagnosis?
New analysis says Alzheimer's preventable in a third, not half of cases
Neurogenesis in Alzheimer's disease promoted by ADSCs transplantation
Four research trials show smell and eye tests offer potential to detect Alzheimer's early
New light shed on primate biology and evolution
Speedy cell by cell reconstruction of an animal's development made possible by imaging technology
Newly-discovered process helps drosophila cope when temperatures get cold
Distinctive developmental origin for a drainage tube in the eye
Researchers identify more than 80 new genes linked to schizophrenia
Life's imprint on DNA now mappable in single cell
Calorie restriction with resveratrol key to kick-starting cell health
Biomedical technologies may be improved by protein in squid skin
Gene identified that controls the timing of precisely ordered events during maturation
Structure of protein vital to cancer development is mapped
Scientists find ancient protein-building enzymes have undergone metamorphosis and evolved diverse new functions
Findings could revolutionise our understanding of timing during development
Study finds friends are genetically similar
New study reveals how cholesterol promotes cancer
Revolutionary technology enables scientists to navigate and analyze complex 3D images
New technology reveals insights into mechanisms underlying amyloid diseases
Wild gorillas provide compelling evidence of olfactory communication in hominoids
Plants respond to predators' chewing sounds
Scripps Florida scientists uncover new compounds that could affect circadian rhythm
Wake-up call for more research into cell metabolism
The 'yin and yang' of malaria parasite development
How tumors weaken blood barrier in brain cancer patients explained
Bone marrow hormone influences metabolism and health
Scientists probe DNA of 'Evolution Canyon' fruit flies and find drivers of change
Does green algae hold a genetic clue to the origin of the sexes?
  • Stickies: 0
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New SMP clients available.
King_N
[H]ard|Folding Administrator


Posts: 101
Points: 2,811,941
Work Units: 6,594

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: 101
Points: 2,811,941
Work Units: 6,594

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: 101
Points: 2,811,941
Work Units: 6,594

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: 101
Points: 2,811,941
Work Units: 6,594

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

Folding@Home
King_N
[H]ard|Folding Administrator


Posts: 101
Points: 2,811,941
Work Units: 6,594

Posted: Fri Oct 29, 2010 04:29 pm
Folding@home has now been running for 10 years.

Quote:
Its with great pleasure that I announce that today is Folding@homes official tenth anniversary. Its been an amazing 10 years, especially in terms of what weve collectively been able to do, and my team and I are grateful for all the contributions by millions of people that has made this possible.


Full article: here

Happy Halloween everyone.
  • Stickies: 0
  • News Articles: 156
  • Pages: 32
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