Method (Automated Setup)

Standard methods such as (abrelax, rasrec and autoNOE) are provided. Methods provide the functionality to generate the appropriate flags and patches for a structure calculation using Rosetta.

• abrelax standard CS-Rosetta protocol[1].
• rasrec iterative CS-Rosetta protocol[2][3][4].
• autoNOE a combination of RASREC, with automatic NOE crosspeak assignment (unpublished).

Methods are defined in subdirectories csrosetta3/flag_library/methods and extensions of the existing methods as well as new methods can easily be integrated into the setup application.

References

1. [shen2008a] Shen Y, Lange OF, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A et al.. 
   2008.  Consistent blind protein structure generation from NMR chemical shift data.. P. Natl. Acad. Sci. USA. 105(12):4685-4690.
2. [raman2010a] Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini JM, Liu G, Ramelot TA, Eletsky A, Szyperski T et al.. 
   2010.  NMR structure determination for larger proteins using backbone-only data.. Science. 327(5968):1014-1018.
3. [Lange2012a] Lange OF, Baker D. 
   2012.  Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation.. Proteins. 80(3):884-895.
4. [Lange2012b] Lange OF, Rossi P, Sgourakis NG, Song Y, Lee H-W, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT et al.. 
   2012.  Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proc Nat Am Soc. (in press)