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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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 MarioG07/27/14 
 Hippiekiller07/26/14 
New test for thyroid cancer increases odds of correct surgery
Some cancer cells are characterized by both high sugar intake and high mobility
Cancer cells allowed to divide even when oxygen-starved by cell's recycling center
Childhood cancer survivors may avoid metabolic syndrome by following a healthy lifestyle
'Five portions of fruit and veg a day are enough'
Could a 'universal' blood test for cancer be on the horizon?
Is the European Union putting cancer research at risk?
Experts at the American Brain Tumor Association's annual conference report findings and dispel myths
Cancer can be driven by epigenetic changes
Nanoparticle stimulate anti-tumor immune responses
SapC-DOPS selectively targets tumor cells in models with brain micrometastases derived from human breast or lung cancer cells
Key molecule identified in flies that adjusts energy use under starvation conditions
New drug target can break down cancer's barrier against treatment
One third of cancer patients are killed by a 'fat-burning' process termed cachexia related to obesity, CNIO researchers say
Treatment identified that prevents tumor metastasis
The "stemness" of individual immune memory cells: a fundamental finding with implications for clinical cell therapy
Protection for skin during cancer radiotherapy provided by natural products from plants
Identifying the carcinogenic potential of chemicals
Study reveals the atomic structure of key muscle component
Cancer drug offers potential for an oral therapy for Alzheimer's disease
New computational method pinpoints gene changes in breast cancer cells
Heart disease risk in childhood cancer survivors 'reduced by healthy lifestyle'
Dyes used to paint new picture of disease
Tumorigenicity in induced pluripotent stem-cell based therapies significantly reduced
Barrett's esophagus less of a risk for those on statins
Research letter examines pacemaker use in patients with cognitive impairment
Dementia 'predicted by slow walking speed and memory problems'
Protein S100B in blood may trigger brain-damaging immune response
Klotho found to be neuroprotective against Alzheimer's disease
Research letter examines pacemaker use in patients with cognitive impairment
Experiences at every stage of life contribute to cognitive abilities in old age
Dementia carers need more medication support, report says
Treatment identified that prevents tumor metastasis
Cancer drug offers potential for an oral therapy for Alzheimer's disease
New mechanism found for neurodegeneration
Therapies focus on areas of memory and learning in the brain to treat obesity
Deleting enzyme favorably impacts behaviors associated with Fragile X syndrome
Potential genetic link found between epilepsy and neurodegenerative disorders
The future of gene therapy for Alzheimer's disease
Explaining the molecular basis of age-related memory loss
Immune cell discovered that plays neuroprotective role in the brain
Amyloid plaque in Alzheimer's disease may affect remote regions of the brain
In older patients with mild cognitive impairment, acupuncture at the Taixi activates cerebral neurons
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
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
Forensic investigations often use dead body feeding larvae
Mathematical modelling could pave way for new chlamydia therapies
High-speed chemical imaging of tissues using enhanced NIST instrument
How gold nanoparticles easily penetrate cells, making them useful for delivering drugs
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
  • Stickies: 0
  • News Articles: 157
  • Pages: 32
Client Version 7(Beta)
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,818,970
Work Units: 6,607

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: 2,818,970
Work Units: 6,607

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: 2,818,970
Work Units: 6,607

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: 2,818,970
Work Units: 6,607

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: 2,818,970
Work Units: 6,607

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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