Folding Forum

I joined F@H b/c I am interested in doing humanitarian work with my PC to help my fellow man, kind of like a good Samaritan. I am Christian and I believe very strongly. I thought that F@H was one way for me to apply God's command "love your fellow man like yourself". I have got my QX9650 CPU working on World Grid tasks (Cure for Schistostomiasis, Malaria, Leishmaniasis, Cancer, Child Cancer and AIDS) and my GTX 580 GPU working a few hours per day on F@H tasks. I read somewhere that F@H helps with finding a cure for cancer and other diseases.

Then today, I got assigned to Project 7660. Here's what the project's description said:

"This project will study the folding and high-energy intermediates of the FF domain, a model protein folding system. What makes this project exciting is that FF has been subject to extensive cutting-edge NMR spectroscopy studies that hope to experimentally reveal folding pathways at atomic resolution, the work of renown experimentalist Lewis Kay. Previously, atomic resolution detail has only been accessible to simulations, like those performed on FAH. Therefore, this provides a unique opportunity for these two methods to benchmark each other -- agreement between both methods would lend a great deal of confidence and scientific credibility to both methods, since each are fairly new and are rapidly pushing the boundaries of what is considered possible in the scientific community"

Looks like this project is a mere comparison of some guys' cool new toys. My GPU is working overtime so that someone can compare his software to someone else's, in other words it is used in a contest to measure someone's e-peen through benchmarking, kind of how computer nerds use Everest or 3D Mark for e-peen fights on MMO Champion boards (e.g. "My PC is da shit, yours sucks").

Please explain to me how my precious GPU time is worth spending here on e-peen projects like the above and not on World Grid doing research on Schistostomiasis, Malaria, Leishmaniasis, Cancer, Child Cancer and AIDS.

Thanks in advance.

I think you're misinterpreting the definition of "benchmark" being used here. This is not comparing one set of software to another. What's being compared is FAH's simulation of the FF folding process and an actual real-life observation of that same process, with that observation being carried out by a well-respected biochemist, not "some guy."

It's important for any type of research to constantly improve the methodology and the tools being used. Next year's projects can't be accomplished with last year's methods. FAH is constantly striving to develop and use improved methods rather than relying on older technology. Some "overhead" needs to be included to accomplish this type of research along with work that directly affects a specific disease.

Hopefully this will be a small portion of the work assigned to you. I do understand and appreciate your concern. There's a feature that is currently being added to the latest version of the client that will allow you to choose what type of project you'd like your contribution to go toward. It's not fully implemented yet (active projects need to be classified on the Servers) but I expect it will be soon. Unfortunately you cannot currently designate your contributions to go ONLY to disease X.

I am not an expert but this is how I understand it.

Folding@Home is a abstract mathematical model of what they think is happening with protein folding. A model has no use unless it matches reality. This project validates the model against experimental reality so that when f@H is modeling "humanitarian" folding that can not be compared against an experiment its results will be trusted. This project may not be directly humanitarian folding but it is a necessary step to be of use when it is.

Comparing images of real proteins to simulated proteins is the only way to assure that simlations like used by fah are accurate predictors.

And because some protein structures develop too quickly to be imaged, simulations are the only way to study them.

It would be wrong to assume that respected researchers at very respected institutions would resort to a lowly size contest.

Here's a really cool abstract from Taming the Complexity of Protein Folding, by Drs. Bowman, Voelz, and Pande, and published in 2011 Current Opinion in Structural Biology:

Protein folding is an important problem in structural biology with significant medical implications, particularly for misfolding disorders like Alzheimer’s disease. Solving the folding problem will ultimately require a combination of theory and experiment, with theoretical models providing a comprehensive view of folding and experiments grounding these models in reality. Here we review progress towards this goal over the past decade, with an emphasis on recent theoretical advances that are empowering chemically-detailed models of folding and the new results these technologies are providing. In particular, we discuss new insights made possible by Markov state models (MSMs), including the role of non-native contacts and the hub-like character of protein folded states.