Huntington's?

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Re: Huntington's?

Postby Jesse_V » Mon Feb 20, 2012 9:58 pm

I like how there's more frequent blog posts. They're always quite fascinating and informative, and I believe that they not only boost the community moral, but they can also be used to demonstrate the project's continued productivity. I've toured the websites of a good number of other distributed computing projects, and seeing a news blog with high-caliber scientific posts on it speaks a lot for the project.

I don't think F@h as a whole could get a Nobel Prize. If there's anyone who would, it would be Dr. Pande, followed closely by Dr. Bowman. However each has already amassed quite a collection of prestigious awards. :D

EDIT: rephrased end of second sentence, added third
Last edited by Jesse_V on Tue Feb 21, 2012 9:14 pm, edited 1 time in total.
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Re: Huntington's?

Postby MtM » Mon Feb 20, 2012 10:10 pm

I think Jesse hit the nail on the head in his first paragraph, though I wouldn't say it different so the 'proof of project's productivity is both boosted in the existing community as well as being there to show to newcomers'. I know there are people ( regulars ) who have asked for these kind of updates, so I don't think it's limited to a morale boost. Allot of people have found it hard to link the results to the project ran, and this blog post is just showing they are listening and making it easier for donors to recognize how their participation has helped, which is great to see.
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Re: Huntington's?

Postby Jesse_V » Mon Feb 20, 2012 10:29 pm

That's an excellent point MtM!
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Re: Huntington's?

Postby Nathan_P » Mon Feb 20, 2012 10:51 pm

Excellent news - seems we are branching out more and more, just one suggestion from me - the project descriptions for these projects are excellent , better than most, however they didn't mention that the projects were focused on Huntington's, some peopel are focused on one disease only - mentioning the ones being worked on can only help recruitment
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Re: Huntington's?

Postby Jesse_V » Mon Feb 20, 2012 11:31 pm

Adam A. Wanderer wrote:Yes, but there's nothing like a Nobel Prize to move your standing up in the scientific community. It just sort of "says something".
But, there are other awards. The "Fields" award for mathematics is only awarded every four years and is considered an even higher award in the Mathematics community. I wonder if Biology has a "super" award. Does anyone know of a really hard to get Biology award?

I'm sure there are a number of presigious biology awards. You might want to look at this page http://folding.stanford.edu/English/Awards Here's one example:
June 2006: Folding@home Principle Investigator Vijay Pande wins the Irving Sigal Young Investigator Award from the Protein Society. From their web site: "The Irving Sigal Young Investigator Award, sponsored by Merck Research Laboratories, recognizes a significant contribution to the study of proteins by a scientist who is in the early stages of an independent career and, generally, not more than 40 years of age at the time of the award. The 2006 awardee is Dr. Vijay Pande (Stanford University) for his unique approach to employing advances in algorithms that make optimal use of distributed computing, which places his efforts at the cutting edge of simulations. The results have stimulated a re-examination of the meaning of both ensemble and single-molecule measurements, making Dr. Pande's efforts pioneering contributions to simulation methodology."
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Re: Huntington's?

Postby Jonazz » Tue Feb 21, 2012 1:28 am

It's always good to see projects that are directly related to a disease. I hope they speed up the search for a cure!
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Re: Huntington's?

Postby Jonazz » Tue Feb 21, 2012 2:31 am

Does anyone know any Huntington forums? Posting this post there might recruit some new members (current Huntington teams can really profit from this).
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Re: Huntington's?

Postby SASinUtah » Tue Feb 21, 2012 4:39 am

The FAH projects related to the above research are between 7700 and 7712. We greatly appreciate the help from all the FAH donors, beta testers, and the rest of the FAH team to make our research on molecular recognition possible.


I agree; if possible, it would be nice to know what general disease type corresponds to the project we are folding. A little personal satisfaction that we made a difference in this or that specific arena. The current descriptions are a little over my head.
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Re: Huntington's?

Postby Jesse_V » Tue Feb 21, 2012 6:34 pm

Well I think we have several options here. You can post any confusing descriptions here and we can try to explain them to you, we could try to convince the appropriate scientist to change the description of an existing project so something that we feel is superior, or we could strive to improve descriptions when the first emerge to the public on the Beta Team forum. I'm currently thinking that the latter option is the most viable, since the scientist involved always seems pretty keen on getting everything just right before releasing it across the rest of F@h and leaving the project alone from there. At least that's how I see things. All three options are doable however. In one case I convinced diwakar to simplify his description a bit, which he did and I think it's very nice now. But if you're confused on a description, post about it and we can help. I think if enough people are confused, maybe they'll change it, who knows. Remember computational molecular biology is intrinsically technical, all the more so if you're doing top-notch science, so I can understand that it's difficult to escape from that.
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Re: Huntington's?

Postby Jorge1950 » Wed Feb 22, 2012 3:16 pm

An interesting reminder. I think what you are referring, it would weigh out brilliantly in biochemistry Dr. Isaac Asimov. In several of his novels "Science Fiction" describes the application of mathematics to describe the behavior of a society. The pinnacle of this approach is expressed in the novel The End of Eternity.

I think the most important of PG, Rosetta and others, is to plant the foundation for the "Process Simulation Cell" by mathematical algorithms. When science and computing, have the ability to do so, it will have gone to another level in understanding cellular processes. I think in the future, PG will be the subject of history by this fact.

Meanwhile, the investigation of small parts such as proteins, will open up gap in the growth process of the basic science of the "mathematical cell". So I am proud to support this project, if only in stage carpentry.

I hope you understand translation. Excuse me.
Sorry for the translation. This aspect, obliges me to very short and concrete sentences. Little by little he will go forward, also in this field.
Thank you for your understanding. Jorge Barrientos
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Re: Huntington's papers and research in general

Postby HuntWarrior » Sat Oct 06, 2012 10:44 am

Dear FAH Management,

For many years (8 to be precise) I have lead a team in respect to contribute to research for HD and other diseases.
I translated almost the whole FAH website into Dutch in 2008 to help to get some more new folders.
I doubt if the attention for HD is big enough at Stanford, but maybe I am wrong.
Our team,that used have 143 members slimmed down to 4 hardcore folders, because motivation died out.
We are about to give up...............Is it still usefull in respect of the above to spend so much money folding, by families and individuals who often have a low income due to HD?
The last (and only?) paper about HD, if i am correct, is the one in 2009 and I get the idea that it is an Alzheimer's priority research project now.
Do you have, or intend to start any, Huntington's research or do you have any papers in the pipeline?
Do you intend to renew the project information wise and ways of working for example: a possible choise what disease you want to be folding for , in respect of those costs?

VijayPande wrote:In terms of big picture highlights, we spent the first 5-6 years working out how to use distributed computing to efficiently tackle protein folding and then applying it to do the first simulations of protein folding reaching the folded state with experimental validation, etc. This was one of our primary goals laid out in the Science section and we're excited to have accomplished that. Part of our work today involves continuing in that direction with more complex systems, continuing to push the state of the art.

The other part of our work is to apply these methods to study disease, especially Alzheimer's Disease (AD) and Huntington's Disease (HD). We are interested in understanding what's going on in these diseases to facilitate a cure. Indeed, our motto in big letters on our web page is "Our goal: to understand protein folding, misfolding, and related diseases," and we are on track for that. One could ask "how do you know if you understand the disease?" A good answer is new small molecule drugs which appear to prevent or minimize the effects of the disease. This too is in the works, with encouraging results in the lab (but it's not time to talk about this publicly until it passes peer review).

However, it takes a long time (often as much as 2-3 years) from the point where we have something interesting in the lab to where we are talking about the results publicly (it has to be validated by ourselves and go through peer review). Our first results on AD and HD will hopefully be coming out soon, i.e. in the next 6 to 12 months or so.

Finally as for a cure -- a cure takes a while to test and develop. First, one has to understand what's going on and that's where basic science comes in and most of what FAH does. However, we and others are excited to take the published results from FAH and apply them to real world problems such as AD and HD and our expectation is that our work could give some critical insights into these diseases, thereby helping to accelerate a cure.



Thanks for your full attention!

Hans van der Leer (team 46113)
Folding for a cure for Huntington's Disease! Team 46113 since 2004 pls look at http://en.hdbuzz.net/ so far in 13 languages and http://hdyo.org in English, Spanish and German so far, interperters are welcome!
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Re: Huntington's?

Postby Jesse_V » Sat Oct 06, 2012 4:07 pm

@HuntWarrior, your questions would best be answered by a member of the PG, but for what it's worth I'll help by telling you what I know.

Alzheimer's has been a priority for the PG for a while now, although there are many scientists using Folding@home and many of them specialize in other diseases. For example, Dr. Kasson is interested in viral infection. If you do a search in the Beta Team Forum, you'll see a number of projects that are geared at HD research. Other information is on the Diseases FAQ page: http://folding.stanford.edu/English/FAQ-Diseases#ntoc7. It's also important to realize that just because a project isn't about HD doesn't mean that it doesn't accelerate a cure for HD. There's a lot of general research to be done, and theories, predictions, or observations from one simulation can carry over into another. From the Diseases FAQ you can see that they're applying their Alzheimer's Disease drug design approaches to HD. I don't know how else to encourage you to stay with us, but there's some indications that conditions may improve for you in the near future.
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Re: Huntington's?

Postby Jonazz » Sat Oct 06, 2012 8:28 pm

Hey Hans,

There are quite some HD projects running now! I remember posting about them in your Huntington Lotgenoten Forum. THis is one of the most interesting times for HD and folding!

I don't have the time to look them up, though.
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Re: Huntington's?

Postby Jonazz » Sun Oct 07, 2012 4:06 am

Project 8051 is active now (unicore and SMP) and is aimed completely at HD:

Huntington's disease is caused due to the presence of poly-glutamine repeats, which associate together to form toxic clumps in neuronal brain cells, leading to cell death and the associated overall neurodegenerative consequences. These repeats of glutamine are attached to one end of the Huntingtin protein. Interestingly, previous publications have shown that a small fragment at the end of the Huntingtin protein, known as N17, accelerates the creation of the toxic clumps. Although there have been several proposed mechanisms of its role, N17's exact role in this process remains largely unknown. In this project, we perform simulations of several fragments of the Huntington protein in an attempt to discover the role of this fragment and its implications in Huntington's disease. For more detailed and technical description of the project, you can read a publication by former pande group member Nicholas W. Kelley (Kelley et. al., Journal of Molecular Biology, 2009).


http://fah-web.stanford.edu/cgi-bin/fah ... ned?p=8051

There were other projects but they seem to be finished. It takes quite a while to go from the results obtained by FAH to a peer reviewed paper.

And don't forget the size of proteins. Abeta is 36–43 amino acids large (long?), Huntingtin is a 3144 (!) amino acids protein. It takes much more advanced software to simulate larger proteins. I do not believe the current F@H methods can tackle a protein as big like Huntingtin. That's whay it is very important that you keep folding!

If you want to talk Dutch, send me a PM.
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Re: Huntington's?

Postby HuntWarrior » Sun Oct 07, 2012 11:08 am

Dear Jesse and Jonasz,

Ofcourse I was aware about what was going on at FAH, however not of the progress of the actual last project.
My knowledge goes further than HD and I realise there are a lot of diseases connected with eachother research wise.
The main problem is to MOTIVATE people, to put on their computer for FAH and spend their precious money (crisis effects and HD) and hear so little in return........( News letter?)
Talking about crisis, due to lack of money our website http://www.huntingtonlotgenoten.nl went down and my activities went more and more to the websites that are mentionned under this message.
In respect of motivation, would it not be an option to be able to pick ones own workunits from the available list?
This was a many heard complaint in out team: " we have to fold to many Alzheimer's Wu's before we come to a HD one"
I do realise it's a long process to come from start and end of a project to a paper and it is the same for Alzheimers that has a higher priority?
Anyway I personally,with some others, will keep up the good work and will keep on (mis)folding, altough the main target in HD research is Gene-silencing (RNAi) now and it looks very promissing!

Thanks Jesse-V for you valuable contribution.

Hans
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