3 ms·
Computational folding is nice, but it's not the only computationally-intensive activity in proteomics. For some proteins with post-transcriptional (ex. alterna
by tomkinstinch 14y ago
Computational folding is nice, but it's not the only computationally-intensive activity in proteomics.
For some proteins with post-transcriptional (ex. alternative splicing) or post-translational modifications (ex. attachment of functional groups, formation of disulfide bridges, proteolytic cleavage) it is difficult or impossible to arrive at the correct folded structures from computation on nucleic acid sequences alone. For such proteins, the structures can be determined experimentally. That means coaxing pure samples of protein to form single crystals and then subjecting the crystals to X-ray diffraction (XRD). Backing out the structural information from the XRD patterns takes serious horsepower (though admittedly not necessarily power with Titan-class interconnects). XRD does not give information about the location of hydrogen atoms in the structure though. For that information you need to do neutron diffraction (the de Broglie wavelength of the neutrons is short). ORNL is actually one of the few places that do neutron diffraction. The OP could connect with some of the neutron folks there and assist them with their research. If not for proteins, maybe for superconductors.
I had a chance to run some Monte Carlo code on some of the machines at ORNL as part of a supercomputing workshop there during the reign of Jaguar. It was an amazing experience. Enjoy it, OP! I hope you get to take a trip there and see all the racks too.
- kayhi 14y agoIf you need an introduction to the neutron folks at Oak Ridge, let me know.
- Xcelerate 14y agoI'll actually be visiting there early February for an experiment. I believe I'm supposed to do some training first. Do you work there?
- kayhi 14y agoI don't, working on a start up instead. Training is standard for those visiting, which can range from 15min to 3hr depending on what you will be doing. If you haven't make sure to leave enough time to complete it before the training office closes.