MichaelsSNoteBook/2008-4-18

04/18/08

Soo iterative rosetta design is running but takes a while.

In the meanwhile, Iam about to analyze the data a little bid more. I made the energy scatter plots today, looks pretty promising.

Stuff I need to do to analyze the data:

investigate following structure pairs

rosetta design

1J2A-1CLH     nomin    high energy NMR
1MG4-1UF0     nomin    X-ray higher energy
1UOH-1TR4     nomin    high energy x-ray > cutoff
1C44-1QND     nomin    high energy x-ray
1GNU-1KOT     nomin    high energy x-ray
1IFB-1AEL     nomin    high energy NMR
1BED-2IJY              high energy X-ray
1IFB-1AEL     E2_1000  NMR energy > cutoff

SCADS

1. 1IFB-1AEL nomin nothing there 2. 1J2A-1CLH nomin no NMR data

should investigate the rest to dobble check to. seems 1IFB-1AEL and 1J2A-1CLH are pretty bad structures.

Additionally, I should divide my stuff into 4 groups. 1. X-ray better before min 2. NMR better before min

3. X-ray better after E2 100 4. NMR better after E2 100

perform for EACH structure pair! It's gonna help me to overlay subsets for every method, maybe I can identify subsets which have the same property for each method (would be awesome)

Check for differences and similarities: some ideas: 1. Fold 2. Sequence lenght 3. rotamericity 4. quality scores 5. Joint RMSD, RMSD, epsilon, fraction core atoms 6. aromatics (and other known issues)

thats it :)