What is the difference between all these protein related projects?

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Aiden

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Message 10673 - Posted: 11 Feb 2006, 20:30:22 UTC

There is Predictor, Rosetta, SIMAP, and World Community Grid. I assume they looking for different things. Sorry if this is a stupid question.
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Message 10682 - Posted: 12 Feb 2006, 0:17:20 UTC

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Message 10683 - Posted: 12 Feb 2006, 1:18:02 UTC - in response to Message 10682.  

thank you
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Message 10724 - Posted: 13 Feb 2006, 10:48:59 UTC

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Message 12730 - Posted: 27 Mar 2006, 22:01:22 UTC

Does anyone know where tne new project Tanpaku fits into this puzzle? Is it looking at folding in a different light?

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Message 16547 - Posted: 18 May 2006, 16:18:18 UTC

Hi, I was looking at Wikipedia\'s entry for Rosetta and Folding @ Home.
I noticed that Dr. Pande from the folding @ home project metnioned:

\"I know Baker and Ranganathan and their work very well and (like the rest of the protein community) find their work very important and impressive. However, Rosetta@home and Folding@Home are addressing very different problems.
Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding). Thus, those methods are not useful for the questions we\'re interested in and the diseases we\'re tackling (Alzheimer\'s Disease and other aggregation related diseases).
Also, one should note that accurate computational protein structure prediction is still very challenging compared to what one can do experimentally, whereas the information obtained from Folding@home on the nature of folding and misfolding pathways matches experiment (eg with quantitative validation in rates, free energy, etc) and then goes beyond what experiment can tell us in that arena. While Rosetta has gone a long way and is a very impressive project, given the choice between a Rosetta predicted structure and a crystal structure, one would always chose the crystal structure. I bet that will be changing due to their great efforts, but that may still be a ways off for that dream to be realized.
So, both are valuable projects IMHO, but addressing very different questions. I think there are some misunderstandings out there, though. Some people think FAH is all about structure prediction (which it is not -- that\'s Rosetta\'s strength) and some think Rosetta is about misfolding related disease (which it\'s not, that\'s Folding@Home\'s strength). Hopefully this post helps straighten some of that out. \"

(and a link mentioned \"Yes, we\'ve made quite a bit of progress on our methods and can now examine proteins on a considerably larger than we could some time ago\")

Is Dr. Pande comments correct, or is there more to it e.g. if the latest changes with Rosetta has increased the scope?
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Message 16550 - Posted: 18 May 2006, 17:27:02 UTC
Last modified: 18 May 2006, 18:24:07 UTC

Tarx, thanks for bringing this up, because I too would like to understand more about this. You can find the complete dialogue at F@H\'s forums.

I found the comments at F@H discussion intriguing, but I don\'t have the knowledge to comment on the subject.

http://forum.folding-community.org/viewtopic.php?p=128665
Someone can also say: \"given the choice between a FAH predicted folding rate and the experimentally measured folding rate, one would always chose the experimental folding rate.\" This is even more true when the folding rate takes years of CPU time to predict. A coarsely predicted 3D structure (may be off by 5-6 A RMSD) is still way more useful than a folding rate that can be measured by FRET with ease. Can you find the cure of AD by knowing the aggregation rate?

Also, there does not exist any practical difficulties using the Rosetta energy function to predict the misfolded structure. Misfolded proteins are proteins in non-native conformations that are low in free energy. Rosetta is an effective energy function (a pretty good one, too) that approximates the free energy, so there is no reason they can\'t do it. It is simply not their goal.



http://forum.folding-community.org/viewtopic.php?t=14019
I know (as well as everyone else in the field of computational biology) your group spent a lot of efforts on calculating the free energy (which is like doing an extremely difficult integral by huge sampling), and that\'s of great interest for many people in physics and chemistry. (all of the papers you pointed out are published on JCP and PRL, all of them physics journals)

However, that is NOT the focus of the computational drug design. The focus of drug design is to predict WHAT drug binds on WHAT pose given a target structure so experimentalists can start making these compounds and do experiments. The exact binding affinity can be measured experimentally with ease. Providing the efficiency, I am not sure the molecular mechanics force field-based free energy calculation can be actually used in drug discovery someday.


(I also pointed to this subject in a previous post in the Protein-ligand interactions and Rosetta applications in drug design)

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Message 16557 - Posted: 18 May 2006, 18:36:09 UTC
Last modified: 18 May 2006, 18:38:42 UTC

Interesting second link there (not just the snip, but the whole thread as there are comments back & forth with the project leader).
Sadly I can\'t say I understand most of the technical parts. The only thing I could do was a quick check on the comment about the papers and did see that although some of the papers are in physics or chemistry journals, there were also papers in \"Journal of Molecular Biology\", \"Biophysical Journal\", \"Annual Review of Biophysics & Biomolecular Structure\" among others (those sound like the right places?).

So much of this discussion I don\'t really understand (not my field at all!). I did see that on their front page they mention \"Your participation can help lead to a cure for these diseases.\" (such as Alzheimer\'s, Mad Cow (BSE), CJD, ALS, Huntington\'s, Parkinson\'s disease, and many Cancers and cancer-related syndromes.) (I guess these are the \"aggregation related diseases\" mentioned).
But that post makes it almost sounds like their aim is something else and their stated aim is more of a way to obtain sufficient computing power (with the side effect of perhaps some advancement in those diseases).
Unfortunately there was no additional reply to that post from the project leader (there was aleady a few) so I can\'t tell if it was a dark secret, something irrelevant or they just got tired of being baited...

And from the Rosetta FAQ \"My research group is involved both in fundamental methods development research and in trying to fight disease more directly.\" - so is the main goal for Rosetta for medical research or to find ways to improve how to do research for future medical research projects?

(Is there a smiley icon for confused? because I\'d use a few right now!)
Yeah, I\'d realy like to know more!
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Message 16562 - Posted: 18 May 2006, 19:33:22 UTC - in response to Message 16557.  
Last modified: 18 May 2006, 19:47:02 UTC

I did see that on their front page they mention \"Your participation can help lead to a cure for these diseases.\" (such as Alzheimer\'s, Mad Cow (BSE), CJD, ALS, Huntington\'s, Parkinson\'s disease, and many Cancers and cancer-related syndromes.) (I guess these are the \"aggregation related diseases\" mentioned).
But that post makes it almost sounds like their aim is something else and their stated aim is more of a way to obtain sufficient computing power (with the side effect of perhaps some advancement in those diseases).


My (non-expert outside observer\'s!) opinion is that the aim of F@H is also fundamental research, on how an why proteins fold.

So perhaps suggesting it\'s working on cures for all the abovementioned diseases may a bit of a stretch. Afterall, this can be said for ANY project which tries to improve our understanding of proteins, as most diseases are manifested at the level of protein activity.

Personally I\'ve found helpful to understand what F@H does the info in What are we ACTUALLY work on?

And from the Rosetta FAQ \"My research group is involved both in fundamental methods development research and in trying to fight disease more directly.\" - so is the main goal for Rosetta for medical research or to find ways to improve how to do research for future medical research projects?


Personally, I think I understand the R@H\'s 3 goals much better:

1/ computationally resolve the tertiary structure of unknown proteins
2/ design proteins (not occuring in nature), e.g. they have created (the 1st?) artificial protein
3/ protein-ligand docking (for drug design, i.e. virtual screening) what AutoDOCK, LigandFit, THINK do

I can readily find a lot of information about each one, there are the biannual CASP as \"benchmark\" etc.
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Message 16569 - Posted: 18 May 2006, 22:03:42 UTC - in response to Message 16562.  

...So perhaps suggesting it\'s working on cures for all the abovementioned diseases may a bit of a stretch. Afterall, this can be said for ANY project which tries to improve our understanding of proteins, as most diseases are manifested at the level of protein activity....

I think each project is keenly aware that to some extent they may be competing for the same volunteer crunchers, and each does not want to lose the people they have to the other project. So some stretching is understandable.

Imho, each project has equal validity as you indicated above, and they both have published results in peer-reviewed scientific journals. So both are advancing fundamental scientific knowledge about proteins, which ultimately will benefit all of us.

Hopefully, each will attract new crunchers to each project so that the overall base of volunteer crunchers increases. I think this is the likely outcome, which will help the field overall! :)
Regards,
Bob P.
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Message 16620 - Posted: 19 May 2006, 6:09:06 UTC

The more we learn about misfolding proteins, the more likely we\'ll find novel approaches to those disease caused by misfolding. I view my contribution to Folding@Home as a contribution to basic science - and if we process enough WUs, then discoveries will be made and projects will be spawned on ways of applying the newfound knowledge.

Rosetta is more of an applied science app; as we improve it, the more likely it\'ll be used to help find treatments/cures. Or be put to use to give close estimates of the shapes of all those proteins that haven\'t been crystalized and analyzed yet.

Both projects need lots more cpu power to get to where they\'re going - soon... but Rosetta is more likely to lead to cures/treatments first.
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Message 16631 - Posted: 19 May 2006, 12:00:27 UTC

Hmmm...
I\'m still wondering about Dr. Pande\'s post (that was put into the Wikipedia)
\"Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding).
...
Some people think FAH is all about structure prediction (which it is not -- that\'s Rosetta\'s strength) and some think Rosetta is about misfolding related disease (which it\'s not, that\'s Folding@Home\'s strength).\"

Is that accurate?

And now also the additional concern (as linked to by Dimitris) noting that folding@home seems to be inefficient for its medical goals...?


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Message 16634 - Posted: 19 May 2006, 13:00:59 UTC
Last modified: 19 May 2006, 13:04:37 UTC

If my understanding is correct, then that statement is correct, as Rosetta, from an amino acid sequence is trying to predict it\'s correct structure, and not investigate misfolded proteins.

It is pretty obvious that given a Rosetta estimate of a structure and a crystallographically proven structure, the crystalographic structure will be preferred. The big but, is that the crystalographic result takes ages and costs a fortune per protein, whereas Rosetta, (and other methods), predictions can be done quickly and cheaply given sufficient computer resources, and the quality of the predictions is improving all the time.
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Message 16641 - Posted: 19 May 2006, 15:47:26 UTC - in response to Message 16634.  

If my understanding is correct, then that statement is correct, as Rosetta, from an amino acid sequence is trying to predict it\'s correct structure, and not investigate misfolded proteins.

It is pretty obvious that given a Rosetta estimate of a structure and a crystallographically proven structure, the crystalographic structure will be preferred. The big but, is that the crystalographic result takes ages and costs a fortune per protein, whereas Rosetta, (and other methods), predictions can be done quickly and cheaply given sufficient computer resources, and the quality of the predictions is improving all the time.


I think that\'s got it. And part of the confusion I believe is that both talk about Alzheimer\'s. As you can imagine, with a disease that is presently uncureable, there are many ideas about possible treatments in the works. And so it sounds like FAH\'s approach is investigating WHY the misfolding occured (i.e. perhaps once we understand this misfolding, we could prevent it from happening). I believe Rosetta\'s approach is to detect that it happened, and see if they can design a new protein that will bind with only the damaged proteins, and either repair or destroy them (i.e. once misfolding has happened, perhaps we can treat it). So, two different approaches to Alzheimer\'s.
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Message 16642 - Posted: 19 May 2006, 15:59:08 UTC - in response to Message 16547.  

Hi, I was looking at Wikipedia\'s entry for Rosetta and Folding @ Home.
I noticed that Dr. Pande from the folding @ home project metnioned:

\"I know Baker and Ranganathan and their work very well and (like the rest of the protein community) find their work very important and impressive. However, Rosetta@home and Folding@Home are addressing very different problems.
Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding). Thus, those methods are not useful for the questions we\'re interested in and the diseases we\'re tackling (Alzheimer\'s Disease and other aggregation related diseases).
Also, one should note that accurate computational protein structure prediction is still very challenging compared to what one can do experimentally, whereas the information obtained from Folding@home on the nature of folding and misfolding pathways matches experiment (eg with quantitative validation in rates, free energy, etc) and then goes beyond what experiment can tell us in that arena. While Rosetta has gone a long way and is a very impressive project, given the choice between a Rosetta predicted structure and a crystal structure, one would always chose the crystal structure. I bet that will be changing due to their great efforts, but that may still be a ways off for that dream to be realized.
So, both are valuable projects IMHO, but addressing very different questions. I think there are some misunderstandings out there, though. Some people think FAH is all about structure prediction (which it is not -- that\'s Rosetta\'s strength) and some think Rosetta is about misfolding related disease (which it\'s not, that\'s Folding@Home\'s strength). Hopefully this post helps straighten some of that out. \"

(and a link mentioned \"Yes, we\'ve made quite a bit of progress on our methods and can now examine proteins on a considerably larger than we could some time ago\")

Is Dr. Pande comments correct, or is there more to it e.g. if the latest changes with Rosetta has increased the scope?



If R@H can tell you the final folded state with in a week then 80% of the problem is solved. Rest related to unfolding.. there are many people working in mutagenesis and other folding approaches using experimental techniques and MD simulations etc.
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Message 16729 - Posted: 20 May 2006, 23:19:29 UTC

Recent thread named \"Wikipedia\" consolidated into this one.
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Message 17407 - Posted: 31 May 2006, 2:00:45 UTC

I asked that question to one of the researchers (Dan) at F@H (note: he works with basic research part of the project rather than the specific medical research part of the project)
\"Just knowing the final, incorrectly folded structure might be enough. But we don\'t know yet. (Incidentally, it just occurred to me that this is one strong reason for government to fund research. There is no way of knowing what the best solution to a problem will be, and there is no telling which part of a biochemical system is the best one to poke around in to cure a disease, until you give a bunch of geeks around the world rooms full of test tubes, jars of buffer salts, and computers, and a bunch of money [\'cause we need beer on the weekends to keep us going]. Only once we understand the problem from a multitude of angles will we know what might be done to fix it.\"
and more...
http://forum.folding-community.org/viewtopic.php?t=15286
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Message 18056 - Posted: 8 Jun 2006, 3:39:33 UTC - in response to Message 16562.  
Last modified: 8 Jun 2006, 3:41:24 UTC

Dimitris Hatzopoulos:
My (non-expert outside observer\'s!) opinion is that the aim of F@H is also fundamental research, on how an why proteins fold. ...
Personally I\'ve found helpful to understand what F@H does the info in What are we ACTUALLY work on? ...

I just read your very nice \"How-To: Join Distributed Computing projects that benefit humanity\" page http://www.hyper.net/dc-howto.html. I noticed that it mentioned \"Comments about F@H in Wikipedia suggest that due to recent developments, \"Folding@Home approach has become somewhat obsolete\"(?). My own measure of useful results would be citations (see later).\"
I saw that Wikipedia was adjusted to correct(?) that statement (that was restated in the discussion page). I\'m not sure where that statement originated from (no sources listed) and it seemed to be more of a random opinion (I did a quick google search and didn\'t find anything like that). As mentioned in this thread (and on the F@H forums) it just looks like two different types of protien related medical research projects with not that much overlap...
Do you know any more about that statement (or its source)? (otherwise perhaps it is just someone trolling?) (and what did you mean about \"(see later)\" )?
I want to include a link to your page for one of the large existing folding@home teams (that I\'m helping to run) as an alternate project, so I want to careful about info regarding their current project is accurate...
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Message 18058 - Posted: 8 Jun 2006, 4:16:39 UTC - in response to Message 18056.  
Last modified: 8 Jun 2006, 4:37:00 UTC

Here is how I described the differences between R@h and F@h from my point of view, as well as my (subjective) reasons to leave F@h for R@h, in another forum:

The two projects are indeed different. They have different goals and they use different methods:

While Folding@home wants to understand how proteins fold, by calculating the intermediate, partly folded states in sequence, Rosetta@home attempts to determine the endpoints of the folding process, i.e., the final 3-dimensional folded shapes of proteins, from their sequence of amino acids (the protein folding problem) - and by reversing this process, to determine amino acids sequences that fold into specific, pre-determined shapes (protein design).

So how does this relate to medical relevance (finding cures):

Since Folding@home studies the details of the folding process, this approach seems particularly suited to study mis-folding which is at the heart of some diseases, Alzheimer\'s comes to mind foremost. Another would be Mad Cow Disease, I am not sure there are many more others but my knowledge on this may be incomplete.
In the case of Rosetta@home I think it is obvious that the capability to design proteins with specific shapes and active sites that are able to perform specific functions in the body has immediate relevance for drug design. Rosetta\'s capability to determine the 3D shapes of proteins from their amino acid sequence on the other hand helps to determine the function those proteins perform in the body and to identify potential drug targets. See the Disease Related Research page at the Rosetta website and the statements by David Baker about \"enzyme design\" that I quoted in my previous post. Info on Alzheimer\'s/mis-folding related research at Rosetta is available here .


Perhaps I should also explain what got me to crunch for Rosetta: I originally participated in Folding@home for a number of years but decided to switch over to Rosetta, shortly after Rosetta went public, when Vijay Pande had spoken favorably of Rosetta and of David Baker\'s work on the Folding@home forum. Here are my reasons for the switch-over:

  • Rosetta at the time was (and still is) the much smaller project in terms of participants - so I felt my contribution would make more of a difference there and it also seemed to be sort of fair that both projects should have access to similar amounts of computing power. So in fact lots more Folding@home participants would have to switch over to Rosetta. ;-)
  • over the years I never really understood how the science done at Folding@home would eventually lead to treatments or cures. With Rosetta the connection to identifying drug targets and to drug design seemed much more obvious.
  • somewhat related to the last point, I never really understood the science behind Folding@home. I mean what is it that we really learn by following the folding path of a protein - I understand the intellectual challenge and fun of being able to do that, but what is the point ? With Rosetta it seemed much easier to understand what the project was after.
  • after participating in Rosetta for a while I also began to enjoy the direct contact to David Baker and the other team members. David Baker is very good at making everyone feel a part of the team and whenever I had a question about the project it was immediately answered. The project is also very willing to take up suggestions by team members.


I thought this might fit in with your discussion...


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Message 18147 - Posted: 8 Jun 2006, 16:56:55 UTC - in response to Message 18056.  
Last modified: 8 Jun 2006, 17:07:55 UTC

I just read your very nice \"How-To: Join Distributed Computing projects that benefit humanity\" page http://www.hyper.net/dc-howto.html. I noticed that it mentioned \"Comments about F@H in Wikipedia suggest that due to recent developments, \"Folding@Home approach has become somewhat obsolete\"(?). My own measure of useful results would be citations (see later).\"
I saw that Wikipedia was adjusted to correct(?) that statement (that was restated in the discussion page). I\'m not sure where that statement originated from (no sources listed) and it seemed to be more of a random opinion (I did a quick google search and didn\'t find anything like that)...


Tarx, I\'m glad you found the HowTo page useful (it\'s been viewed about 48k times sofar and I get quite a few emails about it everyday). I have neglected it a bit, since in recent months I\'ve focused my DC-related contributions on Rosetta (writing the Rosetta page in Wikipedia etc)

About my F@H comment, I referred to the then-current info on F@H in Wikipedia (you can read about it in W\'s \"discussion\" page, with some references, which was wiped out). As I wrote, my personal benchmark would be citations.

Anyway, I\'ve posted all relevant info I\'ve collected (e.g. the discussion with mshen in F\'s forums) in earlier posts in this very thread -here- (and btw I know I should copy it into my HowTo page too).

Basically, (having crunched F@H for a couple of years via GoogleToolBar) my current position is the same with Hoelder1in\'s: \"over the years I never really understood how the science done at Folding@home would eventually lead to treatments or cures. With Rosetta@home the connection to identifying drug targets and to drug design seemed much more obvious.\"

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