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.{{Cite journal|pmid=18326625|year=2008|last1=Shen|first1=Y|last2=Lange|first2=O|last3=Delaglio|first3=F|last4=Rossi|first4=P|last5=Aramini|first5=JM|last6=Liu|first6=G|last7=Eletsky|first7=A|last8=Wu|first8=Y|last9=Singarapu|first9=KK|last10=Lemak|first10=A.|last11=Ignatchenko|first11=A.|last12=Arrowsmith|first12=C. H.|last13=Szyperski|first13=T.|last14=Montelione|first14=G. T.|last15=Baker|first15=D.|last16=Bax|first16=A.|title=Consistent blind protein structure generation from NMR chemical shift data|volume=105|issue=12|pages=4685–90|doi=10.1073/pnas.0800256105|pmc=2290745|journal=Proceedings of the National Academy of Sciences of the United States of America|display-authors=8|bibcode=2008PNAS..105.4685S|doi-access=free}} The software package was later extended to include additional NMR conformational parameters, such as Residual Dipolar Couplings (RDC),{{Cite journal|doi=10.1126/science.1183649|title=NMR Structure Determination for Larger Proteins Using Backbone-Only Data|year=2010|last1=Raman|first1=S.|last2=Lange|first2=O. F.|last3=Rossi|first3=P.|last4=Tyka|first4=M.|last5=Wang|first5=X.|last6=Aramini|first6=J.|last7=Liu|first7=G.|last8=Ramelot|first8=T. A.|last9=Eletsky|first9=A.|last10=Szyperski|first10=T.|last11=Kennedy|first11=M. A.|last12=Prestegard|first12=J.|last13=Montelione|first13=G. T.|last14=Baker|first14=D.|journal=Science|volume=327|issue=5968|pages=1014–8|pmid=20133520|pmc=2909653|display-authors=8|bibcode=2010Sci...327.1014R}} NOE distance restraints,{{cite journal|doi=10.1073/pnas.1203013109|title=Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples|year=2012|last1=Lange|first1=O. F.|last2=Rossi|first2=P.|last3=Sgourakis|first3=N. G.|last4=Song|first4=Y.|last5=Lee|first5=H.-W.|last6=Aramini|first6=J. M.|last7=Ertekin|first7=A.|last8=Xiao|first8=R.|last9=Acton|first9=T. B.|last10=Montelione|first10=G. T.|last11=Baker|first11=D.|pmid=22733734|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=109|issue=27|pages=10873–8|pmc=3390869 |display-authors=8|bibcode=2012PNAS..10910873L|doi-access=free}} pseudocontact chemical shifts (PCS){{Cite journal|url=http://depts.washington.edu/bakerpg/drupal/system/files/schmitz12A.pdf|archive-url=https://wayback.archive-it.org/all/20120712182613/http://depts.washington.edu/bakerpg/drupal/system/files/schmitz12A.pdf|url-status=dead|archive-date=2012-07-12|pmid=22285518|pmc=3638895|year=2012|last1=Schmitz|first1=C|last2=Vernon|first2=R|last3=Otting|first3=G|last4=Baker|first4=D|last5=Huber|first5=T|title=Protein structure determination from pseudocontact shifts using ROSETTA|volume=416|issue=5|pages=668–77|doi=10.1016/j.jmb.2011.12.056|journal=Journal of Molecular Biology}} and restraints derived from homologous proteins.{{Cite journal|last1=Thompson|first1=J M.|last2=Sgourakis|first2=N G.|last3=Liu|first3=G|last4=Rossi|first4=P|last5=Tang|first5=Y|last6=Mills|first6=J L.|last7=Szyperski|first7=T|last8=Montelione|first8=G T.|last9=Baker|first9=D|date=2012-06-19|title=Accurate protein structure modeling using sparse NMR data and homologous structure information|journal=Proceedings of the National Academy of Sciences|language=en|volume=109|issue=25|pages=9875–9880|doi=10.1073/pnas.1202485109|issn=0027-8424|pmid=22665781|pmc=3382498|bibcode=2012PNAS..109.9875T|doi-access=free}} This software can be used together with other molecular modeling protocols, such as docking to model protein oligomers.{{Cite journal|last1=Sgourakis|first1=N G.|last2=Lange|first2=O F.|last3=DiMaio|first3=F|last4=André|first4=I|last5=Fitzkee|first5=N C.|last6=Rossi|first6=P|last7=Montelione|first7=G T.|last8=Bax|first8=A|last9=Baker|first9=D|date=2011-04-27|title=Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings|journal=Journal of the American Chemical Society|volume=133|issue=16|pages=6288–6298|doi=10.1021/ja111318m|pmid=21466200|pmc=3080108|issn=0002-7863}} In addition, CS-ROSETTA can be combined with chemical shift resonance assignment algorithms to create a fully automated NMR structure determination pipeline.{{Cite journal|last=Lange|first=O F.|date=2014-07-01|title=Automatic NOESY assignment in CS-RASREC-Rosetta|journal=Journal of Biomolecular NMR|language=en|volume=59|issue=3|pages=147–159|doi=10.1007/s10858-014-9833-3|pmid=24831340|s2cid=28946271|issn=0925-2738}}{{Cite journal|last1=Evangelidis|first1=T|last2=Nerli|first2=S|last3=Nováček|first3=J|last4=Brereton|first4=A E.|last5=Karplus|first5=P. A|last6=Dotas|first6=R R.|last7=Venditti|first7=V|last8=Sgourakis|first8=N G.|last9=Tripsianes|first9=K|date=2018-01-26|title=Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra|journal=Nature Communications|language=En|volume=9|issue=1|pages=384|doi=10.1038/s41467-017-02592-z|pmid=29374165|pmc=5786013|bibcode=2018NatCo...9..384E|issn=2041-1723}} The CS-ROSETTA software is freely available for academic use and can be licensed for commercial use ([https://csrosetta.chemistry.ucsc.edu/installation installation guide]). A software [https://csrosetta.chemistry.ucsc.edu/node/1 manual] and [https://csrosetta.chemistry.ucsc.edu/tutorials 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 [https://csrosetta.chemistry.ucsc.edu/downloads/toolbox 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.