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Folding@Home Information

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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Active Members
Cancer News
Depressive Symptoms Are Linked To Early Death In Cancer Survivors
Non-Surgical Treatments For Multiple Tumors Move One Step Closer
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Data Addressing Patient And Physician Barriers To Clinical Trials To Be Presented By Experts
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Blocking The Protein-Protein Interaction Which Causes Ewing Sarcoma
Molecular Profiling Timely For Tailoring Cancer Therapy
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Study Findings May Offer New Way To Kill Cancer Cells By Forcing Them Into An Alternative Programmed Death Pathway
In Preclinical Studies, New Drug Enhances Radiation Treatment For Brain Cancer
Chemists Demonstrate Nanoscale Alloys So Bright They Could Have Potential Medical Applications
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Cancer Metastasis Promoted By Tumor-Activated Protein
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Shared Decision Making And How Decision Aids Help Guide Choices For Cancer Screening
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Identifying The Social Needs Of Young People With Cancer
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Alzheimer's News
News From Frontiers In Endocrinology, Microbiology, Physiology
Skin Cancer Link To Lower Risk Of Alzheimer's Disease, Says Study
Assessing The Efficacy Of Different Types Of Training Programs On Cognitive Performance In Elderly Patients
Detect Alzheimer's Disease Years Before Memory Loss And Cognitive Decline Become Apparent
Drug Improves Memory In Mice With Alzheimer's Disease
Obesity-Related Dementia Is Projected To Rise In England
Leukemia Drug Prevents Build-Up Of Toxic Brain Protein
Mutations In Genes That Regulate Cellular Metabolism Found In Families With Ataxia, Dementia And Reproductive Failure
A Patient's Right To Control Genomic Health Information
Association Between Alzheimer's Disease And Removal Of The Synaptic Protein ADAM10
Scientists Bring Clarity To How Most Alzheimer's Drugs Sharpen Brain Performance
Rethinking Therapeutic Strategies That Target APOE To Slow Amyloid Plaque Accumulation And Alzheimer's
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Study Examines Cognitive Impairment In Families With Exceptional Longevity
How Environmental Stimuli And Brain Rhythms Generate Our Neuronal Maps Of The World
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Early Detection Of Alzheimer's Disease Expected In The Next Five To Ten Years
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Mouse Model Sheds New Light On Early Stage Alzheimer's Disease
Biochemistry News
[H]ard|Folding News Articles
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  • News Articles: 142
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Client Version 7(Beta)
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,411,832
Work Units: 6,094

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: 87
Points: 2,411,832
Work Units: 6,094

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: 87
Points: 2,411,832
Work Units: 6,094

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: 87
Points: 2,411,832
Work Units: 6,094

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: 87
Points: 2,411,832
Work Units: 6,094

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

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