I don't know if anyone else caught this nugget in Dr. Bakers journal but it is a doosey.

"Mike Tyka's results from your calculations over the past two weeks on rosetta@home are truly exciting! Many of you have found, starting from an extended chain, structures that are close to the crystal structure but much lower in energy"

I didn't even realize this was possible. I am guessing that even the benchmark for decades for protein structure analysis is somewhat inaccurate and only an estimation. The only other conclusion is in nature some proteins do not fall to very lowest state due to some phenonomon such as quantum effects, vacuumn energy, etc. I suppose I could google it but my guess this would not be an easy issue to find or answer.

Either way if Rosetta@home is truly starting to produce more accurate science than the X-ray method and every other similar program out there then I say I am amazed and grateful to be a small part of a sea change in the biosciences.

I don't know if anyone else caught this nugget in Dr. Bakers journal but it is a doosey.

"Mike Tyka's results from your calculations over the past two weeks on rosetta@home are truly exciting! Many of you have found, starting from an extended chain, structures that are close to the crystal structure but much lower in energy"

I didn't even realize this was possible. I am guessing that even the benchmark for decades for protein structure analysis is somewhat inaccurate and only an estimation. The only other conclusion is in nature some proteins do not fall to very lowest state due to some phenonomon such as quantum effects, vacuumn energy, etc. I suppose I could google it but my guess this would not be an easy issue to find or answer.

Either way if Rosetta@home is truly starting to produce more accurate science than the X-ray method and every other similar program out there then I say I am amazed and grateful to be a small part of a sea change in the biosciences.

i think you're right about the benchmark (i.e. the current techniques) being inaccurate because they have to crystalise the protein to do the x-ray spectroscopy(?) but proteins are generally in liquid (water) and the model is based on them being in water...

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I don't know if anyone else caught this nugget in Dr. Bakers journal but it is a doosey.

"Mike Tyka's results from your calculations over the past two weeks on rosetta@home are truly exciting! Many of you have found, starting from an extended chain, structures that are close to the crystal structure but much lower in energy"

I didn't even realize this was possible. I am guessing that even the benchmark for decades for protein structure analysis is somewhat inaccurate and only an estimation. The only other conclusion is in nature some proteins do not fall to very lowest state due to some phenonomon such as quantum effects, vacuumn energy, etc. I suppose I could google it but my guess this would not be an easy issue to find or answer.

Either way if Rosetta@home is truly starting to produce more accurate science than the X-ray method and every other similar program out there then I say I am amazed and grateful to be a small part of a sea change in the biosciences.

We were really amazed by this too! (Up until recently, I would have considered it heresy to suggest that a structure prediction could be more accurate than a crystal structure!). Right now we are exploring different hypotheses for what could be going on; I will keep you posted!

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Sorta like when the teacher askes what the value of pi is and considers 3.14 the correct answer... but the student comes back with 3.141592653589793

It seems there are three possible reasons for this varience. One is that the BakerLab answer is better then the NMR or crystaline structural analysis, another is that the prior analysis was not done properly, and a third is that the BakerLab answer is NOT better then the other techniques. Isn't it true that we chase lower energy, more-or-less because it's all we've got, but it's not the only factor in the natural structure formation?

How will you proceed to determine which of the 3 is the case here?
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1) Chemical analysis? i.e. see what it binds with? and doesn't bind with?

2) Fire Mike, for heresy? ...then if later found more accurate, you can take the credit ;)

3) Redo the NMR work on this protein to see if prior result is validated?

(I vote against #2. Mike is working hard to both expand the science, and keep the users happy with how their machines behave)

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

That is indeed very exciting. I'm looking forward to more updates on this from the lab, as it might make me move more of my computing power back to Rosetta@home.

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That is indeed very exciting. I'm looking forward to more updates on this from the lab, as it might make me move more of my computing power back to Rosetta@home.

I seem to invariably find that when I move my machines around that is when something exciting happens where I just left!

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Sorta like when the teacher askes what the value of pi is and considers 3.14 the correct answer... but the student comes back with 3.141592653589793

My dad tells the story of how he used to get his math problem wrong for this very reason! Finally his parents and the teacher sat down and figured out what was going on, he was close, just not the exact answer the teacher was looking for. My dad finally had to conform to the teachers way, using only 2 decimal points.

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