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] pseudocontact chemical shifts (PCS)[4] and restraints derived from homologous proteins.[5] This software can be used together with other molecular modeling protocols, such as docking to model protein oligomers.[6] In addition, CS-ROSETTA can be combined with chemical shift resonance assignment algorithms to create a fully automated NMR structure determination pipeline.[7][8] The CS-ROSETTA 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 https://csrosetta.chemistry.ucsc.edu/.

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. Bibcode:2008PNAS..105.4685S. doi:10.1073/pnas.0800256105. PMC 2290745. 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. Bibcode:2010Sci...327.1014R. doi:10.1126/science.1183649. PMC 2909653. 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 of the United States of America. 109 (27): 10873–8. Bibcode:2012PNAS..10910873L. doi:10.1073/pnas.1203013109. PMC 3390869. 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. PMC 3638895. PMID 22285518. Archived from the original (PDF) on 2012-07-12.
  5. Thompson, J M.; Sgourakis, N G.; Liu, G; Rossi, P; Tang, Y; Mills, J L.; Szyperski, T; Montelione, G T.; Baker, D (2012-06-19). "Accurate protein structure modeling using sparse NMR data and homologous structure information". Proceedings of the National Academy of Sciences. 109 (25): 9875–9880. doi:10.1073/pnas.1202485109. ISSN 0027-8424. PMC 3382498. PMID 22665781.
  6. Sgourakis, N G.; Lange, O F.; DiMaio, F; André, I; Fitzkee, N C.; Rossi, P; Montelione, G T.; Bax, A; Baker, D (2011-04-27). "Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings". Journal of the American Chemical Society. 133 (16): 6288–6298. doi:10.1021/ja111318m. ISSN 0002-7863. PMC 3080108. PMID 21466200.
  7. Lange, O F. (2014-07-01). "Automatic NOESY assignment in CS-RASREC-Rosetta". Journal of Biomolecular NMR. 59 (3): 147–159. doi:10.1007/s10858-014-9833-3. ISSN 0925-2738. PMID 24831340.
  8. Evangelidis, T; Nerli, S; Nováček, J; Brereton, A E.; Karplus, P. A; Dotas, R R.; Venditti, V; Sgourakis, N G.; Tripsianes, K (2018-01-26). "Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra". Nature Communications. 9 (1): 384. doi:10.1038/s41467-017-02592-z. ISSN 2041-1723. PMC 5786013. PMID 29374165.
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