Hi everybody,

I'd very much appreciate feedback on this, especially by people who actually know what they're talking about ;)

I tried to explain things as I understood them, but it's very possible that I made errors and I'd like to fix them.

The piece is about proteins, Rosetta@home and computational biology, a new NMR spectrography probe and x-ray crystallography.

http://michaelgr.com/2007/05/24/look-at-them-proteins-a-better-nuclear-magnetic-resonance-probe-and-a-look-at-computational-protein-research/

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This is an excellant article. I like how you cover the various techiniques. I'm not a scientist either, so consider my comments to be those of an experienced Rosetta cruncher.

Simple type-o. This sentence as an extra "most":

It’s long been recognized that most for most proteins the native state is at a thermodynamic minimum.

...but it looks like you are quoting someone there. Perhaps you could elipses out the first most.

The sequence of amino acids is sufficient to determine the native state of a protein.

It would be more descriptive to say that the sequence of amino acids SHOULD BE sufficient... and making that become a reality is really what Rosetta@home is working on.

This makes for astronomical possibilities of combinations, and trying all of them to find the one with the lowest energy would require massive amounts of computing power.

...actually, I don't believe it would be possible to try all of the combinations. Or rather it would take 100s of years. Take 3 to the 1000 power, that is a rough estimate of the number of combinations that exist for a extremely large protein. And so Rosetta@home is actually working on methods that are dramatically more efficient then "trying all of them (combinations)".

So in this case, both the clever design of the software to limit search space and the brute force of distributed computing are required.

Great statement! And poinent quote preceeding it.

gives the desired result without too much side-effects.

You mean too "many" side-effects.

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Where do you plan to publish this? Who is the intended target audience?

If you could incorporate the difficulty, time, and costs of the non-computation methods, times the number of proteins out there that would be useful to understand, that would help show why it is important and useful to continue to develop and extend Rosetta.

It can take weeks to crystalize a protein. And there is no sure-fire method of getting it to do so. And then you x-ray it for like a full day! Along each of the 3 axis, 2 degrees of rotation at a time [source]

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Rosetta Moderator: Mod.Sense

This is an excellant article. I like how you cover the various techiniques. I'm not a scientist either, so consider my comments to be those of an experienced Rosetta cruncher.

Thank you very much for taking the time! I appreciate it.

Simple type-o. This sentence as an extra "most":

It’s long been recognized that most for most proteins the native state is at a thermodynamic minimum.

This is actually from Rosetta's Science FAQ:

https://boinc.bakerlab.org/rosetta/rah_science_faq.php

The sequence of amino acids is sufficient to determine the native state of a protein.

It would be more descriptive to say that the sequence of amino acids SHOULD BE sufficient... and making that become a reality is really what Rosetta@home is working on.

That is also from Rosetta's Science FAQ. Maybe it's time for someone to update it :)

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Where do you plan to publish this? Who is the intended target audience?

If you could incorporate the difficulty, time, and costs of the non-computation methods, times the number of proteins out there that would be useful to understand, that would help show why it is important and useful to continue to develop and extend Rosetta.

So far it's only in for my blog. I write these articles on topics that interest me to help me organize my thoughts and because I learn from doing the research, and to share it with others. But if you would like to modify it so that it is useful to the Rosetta project, I would have no problem with us sharing a byline and it being used elsewhere as long as I also get credit and a link to the original.

Let me know if that interests you.

It can take weeks to crystalize a protein. And there is no sure-fire method of getting it to do so. And then you x-ray it for like a full day! Along each of the 3 axis, 2 degrees of rotation at a time [source]

Yes, I touch on this in the article. Some actually don't crystallize at all, apparently, and that's why nuclear magnetic resonance spectrography must be used.

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