MichaelsSNoteBook/2008-5-8

=05/08/08=

Today was kinda good :).

Made plots for the energy decomposiotion for the fixed backbone design case. Both plots for no min and E2 100 backbone mit were made. Seems, that the bad guy is still the dunbrack term in the rosetta energy function. Also, the vdw and torsion seems to be worse vor some NMR, which leads to higher design energies. Nevertheless, the comparison with the rosetta optimized backbones is gonna be REALLY interesting. Actually, the streE energies vor the E2 100 set come kinda close to the X-ray structures. But for the most cases, the energies are still worse!

Thoughts about the sequence diversity:

A proggie, that computes the entropy of the sequences seems not to be a bad indea. Maybe as a function of included sequences. Jep thats kinda good :).

Also, the pairwise sequence distance matrix of clustalW seems to be promising. It looks like, the designed sequences are kinda far away from the native sequence. The X-ray sequene ist kinda close to the native and clearly seperatable from the NMR sequences. This is for the fixed backbone case. The sequences within the NMR ensemble look pretty close to each other, how their entropy space looks like?

Questions over questions :), Damn, research can be soooo fun :)