I am new to Rosetta, and would like to study it for my side project this year for my Bio 110 class. Could anybody give me a simple breakdown on how this study works? i.e. what are the dependent and independent variables, the control, and if the study has come to any conclusions yet. I would really appriciate andy help !

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This is an interesting post.

I wonder if it would be worth the effort required to prepare a set of web pages to help students in kdog's situation. Such a ready-made project opportunity would add another line of publicity to the project, and you might even get lecturers in other unis promoting your project that way...

Another thought I had when reading kdog's post, comes from something that has been done on CPDN.

The Open University, one of the lead universities behind CPDN, has prepared a distance learning package that can be studied alongside CPDN, and students on that course are recommended to run a single CPDN classic WU as part of their study. This course is only available in some countries, but I understand the course materials can be purchased for delivery anywhere. Further details are here

I don't know if the UW is into distance learning courses at all, but if it is, or if you could team up with another US ini that was, then a course based around practical work of running R@h would both add publicity to the project and possibly even bring in more money in fees than it cost to put together.

Just a couple of ideas - I really don't know enough about the US uni system to know if either of them is remotely feasible.

River~~

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kdog, since you are doing this for a course I am going to make you do a little home-work on your own. On the bakerlab web page you will find the pdf for the original Rosetta citation, which describes how rosetta generates and evaluates different conformations of a given protein sequence:

Simons, K. T., Kooperberg, C., Huang, E., Baker, D. (1997). Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J Mol Biol 268, 209-25.

Have a read and see what you make of that. You should also look at the review
Baker, D. (2000). A surprising simplicity to protein folding Nature 405, 39-42.

and the recent science paper
Toward High-Resolution de Novo Structure Prediction for Small Proteins
Philip Bradley, Kira M. S. Misura, and David Baker
Science 16 September 2005: 1868-1871.

as well as the recent review
Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., Baker, D. (2005). Progress in modeling of protein structures and interactions Science 310, 638-642.

The last 2 are not on our web page yet but your university probably has an institutional subscription to Science.

If you have specific questions once you've read those papers you can post them here, but I suspect most of the answers you want are in there and you will learn far more reading the actual papers than getting glib responses here ;-)

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BTW, just to point you in the right direction, you can consider the jobs currently running on boinc to be control experiments. We are evaluating and improving our methods ability to find the correct (native) conformation of a protein using only its sequence.

The results and improvements made during this control experiment will be used in a real, community-wide, blind experiment called CASP. You can find papers on previous CASP experiments on the bakerlab page.

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When using the term "docking"; Is this used in the sense like 'docking'an animals ears and tail or in the sense of a ship 'docking' at a pier and two spacecraft 'docking' together?
My feeling is for the former sense; though, often, my 'feeling'(?) is completely off base. :)

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Hi Pete,

Hmmm, I'm not sure what it means to dock an animal's ears (But it sounds painful and we don't believe in cruelty to animals here ;-)

Docking a ship is definitely the analogy to protein docking. Two proteins that have complementary surfaces will fit or dock together like 2 pieces of a jigsaw puzzle. The docked complex will have a lower energy (be more stable) than the 2 separate proteins. So to continue with the spaceship analogy, it's like they have eac other in their "tractor beams" and pull together inexorably.

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Hi Pete,

Hmmm, I'm not sure what it means to dock an animal's ears (But it sounds painful and we don't believe in cruelty to animals here ;-)

Docking a ship is definitely the analogy to protein docking. Two proteins that have complementary surfaces will fit or dock together like 2 pieces of a jigsaw puzzle. The docked complex will have a lower energy (be more stable) than the 2 separate proteins. So to continue with the spaceship analogy, it's like they have eac other in their "tractor beams" and pull together inexorably.

>
Thanks for the feedback; It clarifys things for me.
'Docking' an animal's tail or ears is usually done by a veternarian using an anesthesia. It involves removing the tail and/or trimming the ears to a particular shape. (Doberman Pincers ARE born WITH a tail.) However, the operation is still often done by the owner sans anesthesia. It has also been used,(and maybe, still is) instead of branding, to identify ownership of farm animals.
This makes for a good day; I learned something AND taught something. :)

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... So to continue with the spaceship analogy, it's like they have eac other in their "tractor beams" and pull together inexorably.

like this, perhaps?


with thanks to a certtain team for the graphic