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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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FAHcon2012
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,835,860
Work Units: 6,645

Posted: Fri Jun 29, 2012 12:52 am
It has been a busy month for Stanford and the F@HCon.

Quote:
We just had a protein folding conference at Stony Brook University in New York that was extremely encouraging. Both the experimental and theoretical communities are very excited about the results we are generating with Folding@home. In particular, they are excited about (i) our increasing ability to make quantitative connections with experiments and (ii) the long timescale dynamics for large proteins we are now able to capture. For example, we recently succeeded in folding an 80-residue protein on 10 millisecond timescales.


Full Article here


Quote:
To start off FAHcon2012, I gave a talk which included a review of how far Folding@home has come in the last decade. I showed a slide from the very first talk I gave about Folding@home results. That talk was given at Columbia University in August of 2000, and I talked about results from our paper in Science entitled "Screen savers of the world, unite!". That work described the folding of a very small protein (16 amino acids) on a very short timescale (10ns = 10 x 10^-9 seconds!), but still was a major accomplishment for the time.

It's exciting to see how far we've come. One way to think about it is in terms of how long of a time scale and length scale we can simulate for protein folding and protein misfolding diseases (such as Aß aggregation in Alzheimer's Disease):

Time scales: advancing roughly 1000x every 5 years

2000: 1 to 10ns (Fs peptide)

2005: 1 to 10s (villin, Aß aggregation of 4 chains)

2010: 1 to 10ms (NTL9, Lambda repressor)

2015: 1 to 10s?

Just breaking past a microsecond was a big deal. The fact that we can simulate 10's of milliseconds is very exciting, but I'm really excited about where this appears to be leading, allowing us to tackle really challenging and important problems. It would also mean that through a combination of new methods, algorithms, and hardware advances, we've already increased our capabilities by a million fold in just 10 years (2000 to 2010). We're looking forward to hopefully making it a billion fold in 2015!


Full Article here



Quote:
Here's a guest post from Prof. Dr. Xuhui Huang, from the Hong Kong University of Science and Technology.

I had a great time attending the first annual FAH conference and enjoyed the nice summer weather in the Bay area. We had plenty of discussions on the recent progress and future plans of FAH on both scientific and technique sides. I look forward to the future FAH conferences.

In my talk, I reported recent results on two projects from our lab. The first one is the development of a new algorithm for the automatic construction of Markov State Model to investigate the conformational dynamics of multi-body systems. This new algorithm holds great potential to help elucidate the aggregation mechanisms of multiple misfolded peptides to form oligomers and eventually fibrils. In the future, we plan to apply this algorithm to study the human islet amyloid polypeptide (hIAPP) peptides, and its aggregation may result in reducing working β-cells in the Type 2 diabetes patients.


Full Article here




Quote:
Dr. Snow, a new investigator at Colorado State University, gave a presentation focused on upcoming research. A unifying theme of this research is the engineering of new, synthetic proteins with applications in bioenergy & medicine. Specifically, Snow and colleagues are using computational protein design to engineer new cellulase enzymes for more efficient and economical biofuel production. To facilitate these calculations, the Snow group is developing software (SHARPEN) that could be deployed on the Folding@Home network. The technical barriers to developing a SHARPEN F@h core were discussed. Notably, F@h can still contribute to these design problems using existing molecular dynamics simulations.


Full Article here





Folding@home Consortium Conference 2012
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,835,860
Work Units: 6,645

Posted: Wed May 30, 2012 04:06 am
Quote:
Here's a guest post from Dr. Greg Bowman about FAHcon 2012.

I had the opportunity to present two projects at the first Folding@home conference (which was a terrific event!). The first project focused on new protein therapeutics. It has long been known that a protein called IL-2 can help stimulate an immune response, so in theory giving people with diseases like immune deficiencies IL-2 could be tremendously helpful.


Full Article here.


Quote:
On Friday May 25 at Stanford University, we had the first "all-hands on deck" scientific conference for the Folding@home Consortium. The goals were to discuss recent scientific advances, share new techniques for how to better use FAH, as well as to plan for new infrastructure advancements in FAH for the next year.


Full Article here.
Peptoids
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,835,860
Work Units: 6,645

Posted: Tue Apr 24, 2012 04:28 pm
It has been a very busy month for Stanford, several new articles and support for new CPUS has been added to the folding client.

Peptoids

Quote:
One of the projects we're excited about in the Voelz Lab is molecular simulation of synthetic polymers called peptoids. These are biomimetic molecules that can fold like proteins, but they have different structural properties. Several peptoids have been identified that can fold into unique three-dimensional structures, but better computational modeling is needed to identify the driving forces for folding and predict stable peptoid structures. If we can develop tools to do this, peptoids have the potential to be an amazing platform to design functionalized nanostructures that can be used for all kinds of applications, from biotherapeutics to nanomaterials.


Full Article here




Introducing the Voelz lab at Temple, a new member of the FAH Consortium

Quote:
The Voelz Lab just started this past August in the Department of Chemistry at Temple University in Philadelphia, PA. We have just installed two Folding@home servers, and are gearing up to run simulations this summer (which I hope to talk about in future blog posts). In the meantime we have been very lucky to work with the Institute for Computational Molecular Science here at Temple, and a new high-peformance computing cluster to generate some initial data.

One of our interests is using molecular simulation to do computational design of folding and binding properties. Design efforts require looking at folding for lots of different possible protein sequences, which is a natural task for a distributed computing platform like Folding@home. We're working on ways to leverage Markov State Models of conformational dynamics to do efficient estimation of the effects of sequence perturbations. A good starting point to test these ideas are to look at proteins for which many sequences have been characterized, to see if we can predict sequence-dependent changes. Many of these sequence mutations are important in human diseases, so we hope to gain insight into these process as well.


Full Article here




Understanding the folding of hIAPP, the peptide linked to the Type 2 diabetes

Quote:
In addition to the molecular recognition processes, another project his lab is working on at the Folding@home platform is to explore the folding free energy landscape of the human islet amyloid polypeptide (hIAPP). hIAPP (also called amylin) is a 37-residue peptide and its aggregation reduces working β-cells in patients with Type 2 diabetes. As an intrinsically disordered protein, hIAPP monomer does not have a folded global minimum in its folding free energy landscape, but contains many stable local minimums. Thus understanding the nature of these locally metastable states can help us to understand the mechanisms of the hIAPP aggregation, and further design small molecules to inhibit the amyloid formation.[/url]

Full Article




Support for new GPUs (such as Kepler) in the v7 FAH client

[quote]In the past, support for specific GPUs was built into the client. We are working on ways to automatically update this information more easily within the v7 client to support new GPUs, such as the Kepler GPUs which have just came out. While the automatic update isn't ready yet, here is how one can manually do this:

1) Download the GPUs.txt file from [url=https://fah-web.stanford.edu/file-releases/public/GPUs.txt]here


2) Copy the downloaded GPUs.txt file to the client's run directory. The run directory is also called the data directory. In Windows there is a link to this directory in the start menu.

3) After installing the file you must restart your client.

The client has a built-in GPUs.txt which it will use if it does not find one on disk. The client will print a message to the log, very early on, when it reads GPUs.txt from the run directory.

In a future version of the v7 client, this will happen automatically, but for now, we are updating this file on our web site and donors can do this update manually for new hardware.


Full Article here




Receptor Binding by the Influenza Virus

Quote:
The Kasson group has recently published an article in the journal Biochemistry on how influenza binds cell-surface receptors. In this article, we discuss how computational techniques can be used for further analysis of structural and biochemical data on glycan binding by influenza. We review prior work that we have done in collaboration with the Pande group, including research using Folding@home.


Full Article here
Folding@Home v7 Released
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,835,860
Work Units: 6,645

Posted: Tue Mar 27, 2012 09:29 am
It's been a busy month at Stanford.

Folding@Home v7 release

Quote:
This new client is a complete rewrite with the intention to make it much easier for donors to contribute to Folding@home. In particular, the new client unifies the classic, SMP, and GPU clients into a single download. Also, installation (especially of the more high performance clients such as SMP and GPU) is much easier than before. Finally, the revamped viewer should also be a much better user experience for FAH donors.


Download the new client here


FAH simulations lead to a new therapeutic strategy for Alzheimer's Disease

Quote:
I'm very excited to finally talk about some key new results from our lab. These results have been a long time in coming and in many ways represents a major achievement for Folding@home (FAH) in general, demonstrating that the approach we started 10 years ago can make significant steps forward in our long term goals.

Specifically, our long term goals have been to 1) develop new methods to tackle the computational challenges of simulating protein folding; 2) apply these methods to gain new insights into protein folding; 3) use these methods and new insights to simulate Aß protein misfolding, a key process in the toxicity of Alzheimer's Disease (AD); and finally 4) to use those simulations to develop new small molecule drug candidates for AD. In the early years of FAH, we concentrated on the first two goals above. In the last 5-7 years, we have worked to accomplish the third goal. I'm now very excited to report our progress on the last goal using FAH for the development of new therapeutic strategies for AD.


Full article here


Stanford scientists and collaborators boost potency, reduce side effects of IL-2 protein used to treat cancer

Quote:
The utility of a naturally occurring protein given, sometimes to great effect, as a drug to treat advanced cancers is limited by the severe side effects it sometimes causes. But a Stanford University School of Medicine scientist has generated a mutant version of the protein whose modified shape renders it substantially more potent than the natural protein while reducing its toxicity.


Full article here


Protein folding and viral infection
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,835,860
Work Units: 6,645

Posted: Mon Feb 27, 2012 02:00 am
Stanford has released a few new articles.

Protein folding and viral infection

Quote:
Understanding protein folding has many possible areas of biological and biomedical impact. For example, consider one of the major research areas of the Kasson lab at the University of Virginia, namely how the influenza virus infects cells. In the past, Dr. Kasson and Dr. Pande have studied two aspects of this: how the influenza virus recognizes cell-surface receptors so it infects the "right" cell types and how small vesicles fuse.


Dr. Kasson's group is now looking at the function of the viral protein that controls cell entry, a protein called hemagglutinin. The hemagglutinin protein interacts with cell membranes: one piece inserts into the membrane, refolds, and alters the membrane in some unknown manner to promote viral entry. Another piece links the viral and cell membranes and refolds to bring the two together. We are running simulations on Folding@Home to examine each of these pieces. Dr. Kasson's laboratory also looks at these processes experimentally.


Full Article here.


Protein Folding and Molecular Recognition

Quote:
In the past a couple of years, the FAH has greatly helped us on our research on understanding the mechanisms of the molecular recognition processes. Molecular recognition, such as enzymes need to recognize their substrates and drugs have to be designed to specifically bind to certain receptors, is crucial to biology and medicine. Experimentally probing the chemical details of molecular recognition events is challenging, while computer simulations have the potential to provide a detailed picture of such events. With the help of the FAH donors, we are performing large-scale simulations on a group of Periplasmic Binding Proteins aiming to reveal the general relationships between protein structures, its intrinsic dynamics, and mechanism of recognition process.


Full Article here.


LTMD: Key new technology for accelerating folding and misfolding simulations in FAH


Quote:
The Izaguirre Lab at the University of Notre Dame (http://www.nd.edu/~lcls) has been collaborating with the Pande Lab at Notre Dame to produce a new GPU core that leverages the amazing speed of OpenMM implicit-solvent force calculations (the heart of the GPU core in Folding@home) with new Long Timestep Molecular Dynamics (LTMD). This combination currently allows nearly a 10-fold speedup over OpenMM for systems as small as the WW domain (35 residues, 544 atoms) up to the Lambda repressor (80 residues, 2000 atoms). This translates into about 10 microseconds per day of simulation, which brings single trajectory millisecond simulations closer to FAH.

In collaboration with Cauldron Development (lead by Joseph Coffland, primary developer of the Folding@home client and also some cores), we hope to produce a GPU core that might be the first hybrid CPU-GPU core. There are technical questions on how to best do this, and we will engage our enthusiastic beta-tester GPU donors to discuss how to best approach this core when we are closer to production mode.


Full Article here.

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