New CS-Rosetta python interface

Submitted by snerli on Fri, 01/26/2018 - 14:50

Chemical-Shift-Rosetta (CS-Rosetta) is a set of tools that allow efficient use of NMR chemical shifts to perform de novo protein structure determination[1][2]. Currently supported input data include backbone chemical shifts, supplemented by additional NMR-derived structural restraints (NOEs, RDCs, PREs, etc.). CS-Rosetta produces reliable structural ensembles from chemical shifts obtained using either supervised or, more recently, fully automated assignment strategies obtained using the 4D-CHAINS algorithm [3]. To do this, CS-Rosetta performs a selection of protein backbone fragments from high-resolution structures the PDB [4], which are used in conjunction with Rosetta's high-resolution energy function to model the structures of proteins up to 35 kDa. More recent approaches also allow modeling of symmetric oligomeric complexes [5].

The different CS-Rosetta tools can be accessed by NMR scientists through a simple python interface. This site provides a detailed set of instructions, tutorials and comments on the use of the methods.

References

  1. [Nerli2019] Nerli S, Sgourakis NG. 
    2019.  CS-Rosetta. Biological NMR Part A, Methods in Enzymology. 614
  2. [Nerli2018] Nerli S, McShan AC, Sgourakis NG. 
    2018.  Chemical shift-based methods in NMR structure determination. Progress in Nuclear Magnetic Resonance Spectroscopy. 106-107
  3. [Evangelidis2018] Evangelidis T, Nerli S, Nováček J, Brereton AE, P. Karplus A, Dotas RR, Venditti V, Sgourakis NG, Tripsianes K. 
    2018.  Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra. Nature Communications. 9
  4. [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.
  5. [Sgourakis2011a] Sgourakis NG, Lange OF, DiMaio F, Andre I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. 
    2011.  Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.. J. Am. Chem. Soc.. 133(16):6288-6298.