So is F@H rendering proteins.......

[ol' man]

One at a time or is it the same one? Is it constantly making new protein sequences or is as I asked above?

Obviously it has to be different ones all the time but I am just wondering cause I am a chemistry/geology student and I noticed that the molecule/protein is changing form somehwat right on my screen. I know a few of the chemistry programs I have would render molecules after you made them in 2d and really not take that long at all. There are even some that you can make in 3d but still not perfect and then after you were done you could render them it only took a few seconds and I guarentee some of the molecules would be quite large.

?

[Ploaf]

I am pretty sure that it is showing you exactly what it's working on. I noticed some differences between differenct downloads.
Also. If you look at my avatar those are screenshots of the client(villins). The first three are from one download and the rest are from another WU a day later. The ones that we are getting now look to be more tightly folded than before.
This is a guess on my part based on what I've seen.

[ol' man]

What I am trying to say is that yeah it looks different than the one I had last night but why should it take so long to render this molecule? There are certain areas that are perfect for energy levels and that is why the molecule/protein folds or arranges a certain way. I could show you where to get a 3d molecular renderingprogram and it doesn't take long at all to render even a large molecule. This program is how I used to test my old computers for speed. Ironically I found the PPRO 200MHz to be what like 11 times faster at rendering a molecule than a P100 classic.

[Ploaf]

Oh. Now I think know what you're saying. I think they just time it like that. :)

[NedClocker]

The structure of a molecule doesn't change. If it does, it's a different molecule then. The structures of molecules is know. This program is finding how the proteins fold. This is the unknown. Unlike a particular molecule, one protein can have many different ways it structurs, or folds, itself.

This is my best understanding of the topic. Maybe this website can explain it better.

http://www.stanford.edu/group/pandegroup/Cosm/science.html

WHY DO PROTEINS "FOLD"?

However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carryout their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."

One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn how to make synthetic polymers with these properties.

[ol' man]

Here are two proteins that I made. The top one is 3D optimized or rendered for optimum lowest energy confirmation while the bottom one is what it looked like before it was rendered. I am just saying that in a sence this is what F@H is doing but there are other forces involved with this such as Van der Waals forces and such as also hydrogen bonding. You may also find some salt formation between the acidic OH group of the amino acid and the NH3 group of the amino acid too and this will form different folds too. The thing I don't understand is why it takes so long for a wu.

This rendering took my computer only like half a second and in real life before the folding were to begin this is what some of these molecules would look like.

[NedClocker]

Don't know. Maybe because there are so many folds to do. Maybe the program is not really folding, but, rather, working on some diabolical plot to take over the world. :eek: Do we REALLY know what that program is doing? :( Seriously, though, we'll have to ask the people at Stanford, I suppose.

[Tithulta]

Well from what I am understanding you want to know why it takes so long to make a WU. Well this is how I understand it in my very basic terms and failed A&P nightmares.

What you are doing is simply rendering the protein where as what we are doing isn't merely rendering a protein. Our computer are working out how that protein FOLDS IN on itself to #1 see how it does this and#2 to try to understand how it interacts in this state.

That's my take of it and you can take it with a grain of salt since I am only what I am. I semi-intellegent 25yr old who hasn't had a day of molecular-biology in his life, but would like to think he did.. ;)

Anyway really in truly the people over at Stanford could answer you far more intelligently and far more accuracy.

The only thing I can say for certain out it taking so long to produce a WU is that they are doing much more than just rendering a protein. 3d rendering the protein is undoubtedly the easiest part of what it's doing.

[ol' man]

Personally I don't like the sound of this part form above.

One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn how to make synthetic polymers with these properties.

These polymers are exactely what cause mad cows disease as also alzheimers. They are called prions and are basically a substance that binds quite well with the fat in the brain and else where. My org. chem. professor explained it to me quite well in that the prion forms a chain with alanine in the protein forming a long spiral polymer which is lipophilic similar to fats. I am more concerned with them finding a cure than using this info to learn how to make more synthetic protein polymers with this da* charechteristic. Maybe that is what happend in the first da* place. Some shi# a$$ scientist accidently introduced a bacteria that produces these polymeric proteins into the cows and now we have a epidemic. I hate to be a sceptic but why do they need to learn how to make these proteins? They should be finding a way to stop them from forming!

[S_Wilson]

Man can not cure what is not understood unless by accident or coincidence. The odds are against that happening. In reality they have to know how to construct them in order to fix defects or develop cures.