CS-ROSETTA

CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is built on top of the biomolecular modeling and design software called ROSETTA. The name CS-ROSETTA for this branch of ROSETTA stems from its origin in combining NMR chemical shift (CS) data with ROSETTA structure prediction protocols.[1] The software package was later extended to include additional NMR conformational parameters, such as Residual Dipolar Couplings (RDC),[2] NOE distance restraints,[3] and pseudocontact chemical shifts (PCS).[4] The software is freely available for academic use and can be licensed for commercial use (installation guide). A software manual and tutorials are provided on the supporting website www.csrosetta.org.

The ROSETTA software is written in C++. CS-Rosetta is distributed together with a toolbox written in Python that facilitates preparation of input files, setting up of large-scale calculations and post-processing of simulation output. CS-ROSETTA calculations require a substantial computational effort and are usually carried out with 200-2000 parallel processes on computer clusters using the Message Passing Interface (MPI) for communication.

References

  1. ↑ Shen, Y; Lange, O; Delaglio, F; Rossi, P; Aramini, JM; Liu, G; Eletsky, A; Wu, Y; et al. (2008). "Consistent blind protein structure generation from NMR chemical shift data". Proceedings of the National Academy of Sciences of the United States of America. 105 (12): 4685–90. doi:10.1073/pnas.0800256105. PMC 2290745Freely accessible. PMID 18326625.
  2. ↑ Raman, S.; Lange, O. F.; Rossi, P.; Tyka, M.; Wang, X.; Aramini, J.; Liu, G.; Ramelot, T. A.; et al. (2010). "NMR Structure Determination for Larger Proteins Using Backbone-Only Data". Science. 327 (5968): 1014–8. doi:10.1126/science.1183649. PMC 2909653Freely accessible. PMID 20133520.
  3. ↑ Lange, O. F.; Rossi, P.; Sgourakis, N. G.; Song, Y.; Lee, H.-W.; Aramini, J. M.; Ertekin, A.; Xiao, R.; et al. (2012). "Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples". Proceedings of the National Academy of Sciences. 109 (27): 10873–8. doi:10.1073/pnas.1203013109. PMC 3390869Freely accessible. PMID 22733734.
  4. ↑ Schmitz, C; Vernon, R; Otting, G; Baker, D; Huber, T (2012). "Protein structure determination from pseudocontact shifts using ROSETTA" (PDF). Journal of Molecular Biology. 416 (5): 668–77. doi:10.1016/j.jmb.2011.12.056. PMID 22285518.

External links

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