is bigadv really "folding"?

[Punchy]

I was looking at the project descriptions for bigadv, 268x and 690x, and they all seem to start with something like "study how influenza virus recognizes and infects cells". I don't see anything about proteins, folding, or mis-folding, either there or in Kasson's post on results in this section, so I'm wondering if these actually are "folding" at all?

[Jesse_V]

Folding@home studies protein folding and other molecular dynamics. I have informed Dr. Kasson that it would be helpful if there were more information about these projects. A virus is a very tiny thing (is it even alive?) that lands on top of a cell, and injects genetic information into the cell, so that the cell can produce more influenza. I would imagine that there would be some protein-protein interaction/bonding, membrane changes as the virus lands, and then a whole bunch of molecular things that go on inside the cell leading to the cell's complete infection. All of those fall under Folding@home's capabilities, because although F@h primarily studies protein folding, similar techniques can be used to study other events at the molecular level.

[Punchy]

That's not what the web site says. "Our goal: to understand protein folding, misfolding, and related diseases".

It's more than a little misleading to folks who believe they are contributing their resources to fight "diseases such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes". These are people that often have some sort of "folding for the cure" slogan or graphic in their avatars or signatures. I wonder how many of them would be surprised to find out that all bigadv projects are related to influenza and have no protein folding/misfolding component?

Participant since December 2005
Beta-tester since 2007

[jimerickson]

but isn't a virus made of proteins? doesn't it have to "unfold" to infect the cell? i may be missing something though. i am no expert.

[Jesse_V]

Looks like there's a lot of protein events in influenza. http://en.wikipedia.org/wiki/Influenza#Pathophysiology and check out Project 2600: "These projects study how viruses infect cells. We are studying the viral proteins responsible for infection and how they interact with cell membranes."

The software that powers F@h also works for other molecular processes. Look at other project descriptions. We've got things about membrane fusion, project 273 describes molecular transport through a membrane, and project 1475 is all about how membranes are changed by proteins in the cell, 2460 is about proteins inserting into membranes, 3801 is about testing their methods on small molecules, etc. The list goes on. Yes, protein folding is F@h's strong point, but simulations of other molecular dynamics are also active.

[Punchy]

Jesse, I notice you use "we" quite a bit in your posts - are you part of the Pande Group?
Your responses so far indicate to me that my initial statement is correct, and the web site is misleading. I see that you don't want to address that directly.

[Jesse_V]

Jesse, I notice you use "we" quite a bit in your posts - are you part of the Pande Group?
Your responses so far indicate to me that my initial statement is correct, and the web site is misleading. I see that you don't want to address that directly.

I apologize if my "we" usage was misleading. I was referring to "we" as the F@h project in general, but should have used a better word. I'm not part of the Pande Group, I'm just a donor. I've been researching F@h, what it does and how it works, and I've been improving the F@h article on Wikipedia with my findings.

The website is not misleading. F@h is about protein folding, that's why it's called "Folding@home". Protein misfolding is very tied to many diseases, and so that's why we participate in this project. If bigadv is all about influenza recongizing and infecting cells as you say, and I've pointed out that influenza is a virus, and that virus use proteins for their recognition of cells, then bigadv is indeed about folding, which is what this topic asked in the first place. I just wanted to point out that in addition to protein folding, to lesser degree the Pande Group (as evident by the information they post on their website and the scientific publications) performs studies of other molecular dynamics. There have also been projects about protein structure prediction (viewtopic.php?f=17&t=14179#p139017 and http://folding.typepad.com/news/2007/09 ... lenge.html) but the website is not misleading because the majority of the research is focused towards protein folding, aggregation, and related diseases.

[gwildperson]

Somewhere on the website, it talks about proteins being all about "shape" and learning about "folding" is pretty much equivalent to learning how and why a protein acquires a particular shape.

The virus is only able to infect certain cells because it has a shape that is compatible with the shape of the proteins on the surface of that cell. it's infecting. How does a bird flu or a swine flu morph into a flu that can infect humans and why do certain flu viruses never infect humans and how do you build a vaccination that teaches the immune system to attach next year's flu virus? Knowing more about folding speaks directly to these questions.

[mdk777]

Really?

Why would anyone care about the flu virus?
The 1918 version only killed 50 to 100 million people. (more than were killed in WWI).

Come on, at least 200 people world-wide have been confirmed to die from Creutzfeldt–Jakob disease

lets not get all crazy and apply pure research to actual emerging epidemics. Folding research should obviously only apply to diseases that are caused by a mis-folded protein. Applying the understanding of protein folding in general to other disease prediction and prevention should be avoided. Next thing you know, someone will start to apply the general understanding to other diseases like Malaria.
http://www.dailymail.co.uk/health/artic ... -heel.html

This lack of focus could really get out of hand.

[Punchy]

Honestly, since this site is frequented mostly by Stanford apologists, I didn't expect anyone to agree. mdk's in particular is most typical.

All I asked for is some honesty about what research is actually being performed. That's really deserving of a massive dump of SARCASM? You don't think people have the right to choose where their resources are used?

A person comes to folding.stanford.edu with an interest in helping contribute to the cures of particular diseases and sees "diseases such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes". Would it be wrong of them to be surprised that the only focus of the most resource-intensive SMP projects is influenza?

To me, it's just another indicator of the lack of transparency here, usually couched in the "lack of resources" defense. How many years has bigadv and influenza research been done? And nobody could bother to update the main page?

[Jesse_V]

How can be sure that influenza research will have implications only in influenza?

[jimerickson]

influenza research has been done since the inception of bigadv, at least thats how i remember it. wasn't p2684 influenza? its been awhile, so i could be wrong but i don 't recall anything being hidden from donors.

[Punchy]

Yes, 268x as I mentioned in my first post, are all influenza related.

You're all still missing the point. It's not mentioned on the MAIN PAGE!

Maybe my expectations are just too high. I can go to my WCG page and select several cancer projects without being concerned that I will be doing erectile dysfunction research. The connection between the user's choices and the work is right up front. Maybe instead of moving towards flags for giant, big, medium and small SMP as some have suggested, the client should move towards flags for choices of diseases and research areas instead.

[Macaholic]

See research papers 61, 70, and 73 for more details.

[Jesse_V]

You're all still missing the point. It's not mentioned on the MAIN PAGE!

All right. The main page should be kept very simple, so as to not be overwhelming to newcomers. I agree though that it ought to be mentioned in the Disease Studied FAQ, that really is a better place for it. Here's a list of all diseases that I have found that F@h studies, but there could be a bit more:

Alzheimer's disease, Parkinson's disease, cancer, Creutzfeldt–Jakob disease, Huntington's disease, cystic fibrosis, sickle-cell anaemia, HIV, Chagas disease, influenza, osteogenesis imperfecta, malaria, and alpha 1-antitrypsin deficiency. Note that autism has been tied to protein folding as well, and F@h's research also has some big implications into antibiotics.

Perhaps the main page should say "Protein folding is linked to disease, such as Alzheimer's, ALS, Huntington's, Parkinson's disease, many cancers, and other diseases" or something like that. What do you suggest it should say? What set of the diseases should be mentioned, and in what order? If you have a suggestion, a detailed solution might be better, although there's no guarantee that it will go through but you can always try.