April 1st 2008
As usuall, meeting with Amy was pretty helpful. I have a couple of new tasks for the next couple of days.
I. Search in the liturature for every X-ray vs. NMR results available. Everything that has to do with quality validation could be useful. Amy also suggested the search after rotamer library paper (look for NMR stuff) and the authors Kuhlmann and Richardson JS.. Current opinnion structure biology should also be checked.
II. Find 5 - 10 structure pairs which are not biased by the more than 0.5 fraction of core heavy atoms. Could be though, I contactec Mike Andrec, maybe he has still a list of the pairs he used after different filtering steps.
III. Break up the rosetta energies to investigate, what can cause the bias towards X-ray structures.
IV. Break up the testset in cases:
A. Better NMR before min B. Better X-ray before min C. Better NMR after E2 100 D. Better X-ray after E2 100
and look what you find :)
V. Start writing the paper (methods and introduction? maybe already results ^^)