Project 7611

[Alan C. Lawhon]

I just noticed my computer is crunching a Project 7611 WU. I read the Project 7611 technical description and noted this very interesting information:

Project 7611

This project involves additional sampling of the FiP35 WW domain shot from the ultra-long trajectories run by DE Shaw on their new supercomputer ANTON. We are testing the differences between these new ultra-long trajectories and shorter ones from FAH, to test how simulations run on FAH stack up to more traditional methods.

I'm not enough of a molecular biologist (or computer scientist) to understand the FiP35 WW domain, but I did notice that this particular protein appears to be substantial, comprising 13,564 atoms. (I suppose that's a relatively large molecule to simulate.) The thing that is so fascinating (to me) about this particular project will be reading the forthcoming paper that compares and contrasts FAH's "brute force" methodology to ANTON's more traditional "experimental" approach and how strongly the results of the two methodologies correlate.

I'm not sure how large and how "CPU intensive" simulation of the alpha synuclein protein (and how suitable a job for ANTON) simulating that protein would be. What I'm hoping is that ANTON (backed up by FAH) can go after the alpha synuclein protein sometime in the near future. Misfolding of the alpha synuclein protein is strongly suspected as a factor in Parkinson's disease. My foster sister has Parkinson's, so I would really like to see ANTON (and FAH) simulate this protein and unravel its mysteries.

I'm curious about alpha synuclein. Is the "problem" (at present) that the protein is simply too large and too complex to simulate? Would doing an alpha synuclein project (on both ANTON and FAH) require more processing power - and require years as opposed to months - of processing time? (Is this a common problem with some of the suspected disease causing proteins - that they're simply too large and computationally challenging to simulate at this time?)

I noted from the technical description of another [current] FAH project that one of the research efforts is testing a new algorithm which has the potential to speed up simulations (on current hardware) by a factor of 100 times. (Heck, a 10 to 20 fold increase would be wonderful - a 100x increase is a gift from God!) If testing results validate this new algorithm, that would be great as it should (one hopes) bring alpha synuclein into the crosshairs. This is all very exciting and very encouraging. Keep up the good work Dr. Pande! You've got a great team doing great work.

Question: When might we expect (ballpark estimate) to be seeing a paper on the results of Project 7611? (That should be a very interesting read.)

[Jesse_V]

The paper already exists: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227799/ but I think 7611 is some kind of follow-up or continuation of their tests. I've summarized that paper a bit in the paragraph on Anton in the F@h article: http://en.wikipedia.org/wiki/F@h#Compar ... simulators
There's also a bit of comparison on the Simulation FAQ: http://folding.stanford.edu/English/FAQ ... tion#ntoc8 and this blog post relates: http://folding.typepad.com/news/2011/10 ... aches.html

Alpha synuclein relates to Alzheimer's. http://en.wikipedia.org/wiki/Alpha_synuclein

The speedup relates to this paper, but I think they're continuing to test it. viewtopic.php?f=17&t=22586 and viewtopic.php?f=17&t=18884 are related threads if you're interested.

[Alan C. Lawhon]

The paper already exists: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227799/ but I think 7611 is some kind of follow-up or continuation of their tests. I've summarized that paper a bit in the paragraph on Anton in the F@h article: http://en.wikipedia.org/wiki/F@h#Compar ... simulators
There's also a bit of comparison on the Simulation FAQ: http://folding.stanford.edu/English/FAQ ... tion#ntoc8 and this blog post relates: http://folding.typepad.com/news/2011/10 ... aches.html

Alpha synuclein relates to Alzheimer's. http://en.wikipedia.org/wiki/Alpha_synuclein

The speedup relates to this paper, but I think they're continuing to test it. viewtopic.php?f=17&t=22586 and viewtopic.php?f=17&t=18884 are related threads if you're interested.

Jesse:

Thanks! Lots of good info to chew on here. This may not happen during my lifetime, (I'm getting on up in years), but the rate of these advances compels me to believe that genetic based diseases that have plagued mankind for millenia are on their way out. There is this http://spectrum.ieee.org/biomedical/dev ... ine-and-me recent article in IEEE Spectrum that just makes my head swim.