Structure Calculation Using CS-Rosetta - Revision history

Oliver.lange: /* References */

2012-06-14T12:43:32Z

References

← Older revision		Revision as of 12:43, 14 June 2012
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	== '''References''' ==		== '''References''' ==
	<references/>		<references/>
	[http://www.ncbi.nlm.nih.gov/pubmed/19034676?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 2.  Shen, Y., Vernon, R., Baker, D. and Bax, A. (2009) De novo protein structure determination from incomplete chemical shift assignments.  <span style="font-style: italic;">J</span>''. Biomol. NMR 43'', 63-78.]

Oliver.lange: /* Protocol for running CS-ROSETTA at CABM */

2012-06-14T12:43:02Z

Protocol for running CS-ROSETTA at CABM

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	</pre>		</pre>
	=== Protocol for running CS-ROSETTA at CABM<br> ===		=== Protocol for running CS-ROSETTA at CABM<br> ===

			'''NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]
			'''

	Start from a chemical shift file in bmrb 2.1 format including the complete header.    Here is an example bmrb file in the correct format, the scripts are rather unforgiving of format inconsistencies.<br>		Start from a chemical shift file in bmrb 2.1 format including the complete header.    Here is an example bmrb file in the correct format, the scripts are rather unforgiving of format inconsistencies.<br>

Oliver.lange: /* CS-ROSETTA Protocol at UB */

2012-06-14T12:42:23Z

CS-ROSETTA Protocol at UB

← Older revision		Revision as of 12:42, 14 June 2012
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	== '''CS-ROSETTA Protocol at UB''' ==		== '''CS-ROSETTA Protocol at UB''' ==

			'''NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]
	== '''NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]		'''
	''' ==

	=== '''Random Coil Index Prediction''' ===		=== '''Random Coil Index Prediction''' ===

Oliver.lange: /* CS-ROSETTA Protocol at UB */

2012-06-14T12:41:37Z

CS-ROSETTA Protocol at UB

← Older revision		Revision as of 12:41, 14 June 2012
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	== '''CS-ROSETTA Protocol at UB''' ==		== '''CS-ROSETTA Protocol at UB''' ==

	'''NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]
	'''		== '''NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]
			''' ==

	=== '''Random Coil Index Prediction''' ===		=== '''Random Coil Index Prediction''' ===

Oliver.lange: /* CS-ROSETTA Protocol at UB */

2012-06-14T12:41:02Z

CS-ROSETTA Protocol at UB

← Older revision		Revision as of 12:41, 14 June 2012
Line 12:		Line 12:
	== '''CS-ROSETTA Protocol at UB''' ==		== '''CS-ROSETTA Protocol at UB''' ==

	NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]		'''NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]
			'''
	=== '''Random Coil Index Prediction''' ===		=== '''Random Coil Index Prediction''' ===

Oliver.lange: /* CS-ROSETTA Protocol at UB */

2012-06-14T12:39:51Z

CS-ROSETTA Protocol at UB

← Older revision		Revision as of 12:39, 14 June 2012
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	== '''CS-ROSETTA Protocol at UB''' ==		== '''CS-ROSETTA Protocol at UB''' ==

			NOTE: the CS-ROSETTA protocol described here is outdated. With creation of the [http://www.csrosetta.org/node/1151 CS-Rosetta toolbox] the process has been greatly simplified. Follow instructions for installation and usage on [http://www.csrosetta.org www.csrosetta.org]

	=== '''Random Coil Index Prediction''' ===		=== '''Random Coil Index Prediction''' ===
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	submits the job.  Depending on the cluster usage, several instances of the above command can be launched to occupy as many cpu as possible.  Rosetta handles the output bookkeeping and increments the decoy counter automatically so that the chosen number of decoys are calculated by the available CPUs.  The number of decoys can be adjusted in the runRosetta script (e.g. -nstruct 1000).<br>		submits the job.  Depending on the cluster usage, several instances of the above command can be launched to occupy as many cpu as possible.  Rosetta handles the output bookkeeping and increments the decoy counter automatically so that the chosen number of decoys are calculated by the available CPUs.  The number of decoys can be adjusted in the runRosetta script (e.g. -nstruct 1000).<br>

	<br>		<br>

	== '''Files for Download''' ==		== '''Files for Download''' ==

Oliver.lange: /* References */

2012-06-14T12:37:11Z

References

← Older revision		Revision as of 12:37, 14 June 2012
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	== '''References''' ==		== '''References''' ==
	<references/>		<references/>
			[http://www.ncbi.nlm.nih.gov/pubmed/19034676?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 2.  Shen, Y., Vernon, R., Baker, D. and Bax, A. (2009) De novo protein structure determination from incomplete chemical shift assignments.  <span style="font-style: italic;">J</span>''. Biomol. NMR 43'', 63-78.]
	[http://www.ncbi.nlm.nih.gov/pubmed/18326625?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 1.  Shen, Y., Lange, O., Delaglio, F., Rossi, P., Aramini, J.M., Liu, G., Eletsky, A., Wu, Y., Singarapu, K.K., Lamak, A., Ignatchenko, A., Arrowsmith, C.H., Szyerpski, T., Montelione, G.T., Baker, D and Bax, A. (2008) Consistent blind protein structure generation from NMR chemical shift data. ''Proc. Natl Acad Sci. 105'', 4585-4590.]

	[http://www.ncbi.nlm.nih.gov/pubmed/19034676?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 2.  Shen, Y., Vernon, R., Baker, D. and Bax, A. (2009) De novo protein structure determination from incomplete chemical shift assignments.  <span style="font-style: italic;">J</span>''. Biomol. NMR 43'', 63-78.]

	[http://www.ncbi.nlm.nih.gov/pubmed/20133520?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 2.  Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D. (2009) NMR structure determination for larger proteins using backbone-only data.  <span style="font-style: italic;">Science</span>''. 327'', 1014-8.]

	~~<br>~~

Oliver.lange: /* References */

2012-06-14T12:36:18Z

References

← Older revision		Revision as of 12:36, 14 June 2012
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	== '''References''' ==		== '''References''' ==
			<references/>

	[http://www.ncbi.nlm.nih.gov/pubmed/18326625?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 1.  Shen, Y., Lange, O., Delaglio, F., Rossi, P., Aramini, J.M., Liu, G., Eletsky, A., Wu, Y., Singarapu, K.K., Lamak, A., Ignatchenko, A., Arrowsmith, C.H., Szyerpski, T., Montelione, G.T., Baker, D and Bax, A. (2008) Consistent blind protein structure generation from NMR chemical shift data. ''Proc. Natl Acad Sci. 105'', 4585-4590.]		[http://www.ncbi.nlm.nih.gov/pubmed/18326625?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 1.  Shen, Y., Lange, O., Delaglio, F., Rossi, P., Aramini, J.M., Liu, G., Eletsky, A., Wu, Y., Singarapu, K.K., Lamak, A., Ignatchenko, A., Arrowsmith, C.H., Szyerpski, T., Montelione, G.T., Baker, D and Bax, A. (2008) Consistent blind protein structure generation from NMR chemical shift data. ''Proc. Natl Acad Sci. 105'', 4585-4590.]

Oliver.lange: /* Introduction */

2012-06-14T12:35:37Z

Introduction

← Older revision		Revision as of 12:35, 14 June 2012
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	== '''Introduction''' ==		== '''Introduction''' ==
	CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is build on top of the biomolecular modeling package ROSETTA. The name CS-ROSETTA for this branch of ROSETTA stems from its origin in combining backbone chemical shift (CS) data with ROSETTA structure prediction protocols, which allowed accurate predictions of 3D protein structures up to 15 kDa in size<ref>Y. Shen, O.F. Lange, F. Delaglio, P. Rossi, J.M. Aramini, G. Liu, A. Eletsky, Y. Wu, K.K. Singarapu, A. Lemak, A. Ignatchenko, C.H. Arrowsmith, T. Szyperski, G.T. Montelione, D. Baker, A. Bax, Consistent blind protein structure generation from NMR chemical shift data. Proceedings Of The National Academy Of Sciences Of The United States Of America, 2008, 105, 4685–4690.</ref> . The software package was later extended to include additional NMR conformational parameters, such as Residual Dipolar Couplings (RDC)<ref>S. Raman, O.F. Lange, P. Rossi, M. Tyka, X. Wang, J.M. Aramini, G. Liu, T.A. Ramelot, A. Eletsky, T. Szyperski, M.A. Kennedy, J. Prestegard, G.T. Montelione, D. Baker, NMR structure determination for larger proteins using backbone-only data. Science, 2010, 327, 1014–1018.</ref>, NOE distance restraints<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>, and pseudocontact chemical shifts (PCS)<ref>C. Schmitz, R. Vernon, G. Otting, D. Baker, T. Huber, Protein structure determination from pseudocontact shifts using ROSETTA. Journal of molecular biology, 2012, 416, 668–677.</ref>. The original CS-Rosetta protocol was based on a combination of ROSETTAs de-novo structure prediction protocol featuring Monte-Carlo assembly of molecular fragments and subsequent full-atom relax. Later an iterative protocol for '''R'''esolution '''A'''dapted '''S'''tructural '''Rec'''ombination ('''RASREC''') was developed and shown to significantly extend the convergence of CS-ROSETTA towards larger structures. A combination of RASREC and sparse NOE distance restraints from ILV-labelled proteins was shown to allow accurate 3D structure determination for proteins up to 40kDa<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>.		CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is build on top of the biomolecular modeling package ROSETTA. The name CS-ROSETTA for this branch of ROSETTA stems from its origin in combining backbone chemical shift (CS) data with ROSETTA structure prediction protocols, which allowed accurate predictions of 3D protein structures up to 15 kDa in size<ref>Y. Shen, O.F. Lange, F. Delaglio, P. Rossi, J.M. Aramini, G. Liu, A. Eletsky, Y. Wu, K.K. Singarapu, A. Lemak, A. Ignatchenko, C.H. Arrowsmith, T. Szyperski, G.T. Montelione, D. Baker, A. Bax, Consistent blind protein structure generation from NMR chemical shift data. Proceedings Of The National Academy Of Sciences Of The United States Of America, 2008, 105, 4685–4690.</ref> . The software package was later extended to include additional NMR conformational parameters, such as Residual Dipolar Couplings (RDC)<ref>S. Raman, O.F. Lange, P. Rossi, M. Tyka, X. Wang, J.M. Aramini, G. Liu, T.A. Ramelot, A. Eletsky, T. Szyperski, M.A. Kennedy, J. Prestegard, G.T. Montelione, D. Baker, NMR structure determination for larger proteins using backbone-only data. Science, 2010, 327, 1014–1018.</ref>, NOE distance restraints<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>, and pseudocontact chemical shifts (PCS)<ref>C. Schmitz, R. Vernon, G. Otting, D. Baker, T. Huber, Protein structure determination from pseudocontact shifts using ROSETTA. Journal of molecular biology, 2012, 416, 668–677.</ref>. The original CS-Rosetta protocol was based on a combination of ROSETTAs de-novo structure prediction protocol featuring Monte-Carlo assembly of molecular fragments and subsequent full-atom relax. Later an iterative protocol for '''R'''esolution '''A'''dapted '''S'''tructural '''Rec'''ombination ('''RASREC''') was developed<ref>O.F. Lange, D. Baker, Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins: Structure, Function, and Bioinformatics, 2012, 80, 884–895. </ref> and shown to significantly extend the convergence of CS-ROSETTA towards larger structures. A combination of RASREC and sparse NOE distance restraints from ILV-labelled proteins was shown to allow accurate 3D structure determination for proteins up to 40kDa<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>.

	The software is freely available for academic use and can be licensed for commercial use ([http://www.csrosetta.org/installation installation guide]). A software [http://www.csrosetta.org/manual manual] and [http://www.csrosetta.org/tutorials tutorials] are provided on the supporting website [http://www.csrosetta.org www.csrosetta.org].		The software is freely available for academic use and can be licensed for commercial use ([http://www.csrosetta.org/installation installation guide]). A software [http://www.csrosetta.org/manual manual] and [http://www.csrosetta.org/tutorials tutorials] are provided on the supporting website [http://www.csrosetta.org www.csrosetta.org].

Oliver.lange: /* Introduction */

2012-06-14T12:34:52Z

Introduction

← Older revision		Revision as of 12:34, 14 June 2012
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==
	CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is build on top of the biomolecular modeling package ROSETTA. The name CS-ROSETTA for this branch of ROSETTA stems from its origin in combining backbone chemical shift (CS) data with ROSETTA structure prediction protocols, which allowed accurate predictions of 3D protein structures up to 15 kDa in size<ref>Y. Shen, O.F. Lange, F. Delaglio, P. Rossi, J.M. Aramini, G. Liu, A. Eletsky, Y. Wu, K.K. Singarapu, A. Lemak, A. Ignatchenko, C.H. Arrowsmith, T. Szyperski, G.T. Montelione, D. Baker, A. Bax, Consistent blind protein structure generation from NMR chemical shift data. Proceedings Of The National Academy Of Sciences Of The United States Of America, 2008, 105, 4685–4690.</ref> . The software package was later extended to include additional [[NMR]] conformational parameters, such as Residual Dipolar Couplings (RDC)<ref>S. Raman, O.F. Lange, P. Rossi, M. Tyka, X. Wang, J.M. Aramini, G. Liu, T.A. Ramelot, A. Eletsky, T. Szyperski, M.A. Kennedy, J. Prestegard, G.T. Montelione, D. Baker, NMR structure determination for larger proteins using backbone-only data. Science, 2010, 327, 1014–1018.</ref>, NOE distance restraints<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>, and pseudocontact chemical shifts (PCS)<ref>C. Schmitz, R. Vernon, G. Otting, D. Baker, T. Huber, Protein structure determination from pseudocontact shifts using ROSETTA. Journal of molecular biology, 2012, 416, 668–677.</ref>. The original CS-Rosetta protocol was based on a combination of ROSETTAs de-novo structure prediction protocol featuring Monte-Carlo assembly of molecular fragments and subsequent full-atom relax. Later an iterative protocol for '''R'''esolution '''A'''dapted '''S'''tructural '''Rec'''ombination ('''RASREC''') was developed and shown to significantly extend the convergence of CS-ROSETTA towards larger structures. A combination of RASREC and sparse NOE distance restraints from ILV-labelled proteins was shown to allow accurate 3D structure determination for proteins up to 40kDa<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>.		CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is build on top of the biomolecular modeling package ROSETTA. The name CS-ROSETTA for this branch of ROSETTA stems from its origin in combining backbone chemical shift (CS) data with ROSETTA structure prediction protocols, which allowed accurate predictions of 3D protein structures up to 15 kDa in size<ref>Y. Shen, O.F. Lange, F. Delaglio, P. Rossi, J.M. Aramini, G. Liu, A. Eletsky, Y. Wu, K.K. Singarapu, A. Lemak, A. Ignatchenko, C.H. Arrowsmith, T. Szyperski, G.T. Montelione, D. Baker, A. Bax, Consistent blind protein structure generation from NMR chemical shift data. Proceedings Of The National Academy Of Sciences Of The United States Of America, 2008, 105, 4685–4690.</ref> . The software package was later extended to include additional NMR conformational parameters, such as Residual Dipolar Couplings (RDC)<ref>S. Raman, O.F. Lange, P. Rossi, M. Tyka, X. Wang, J.M. Aramini, G. Liu, T.A. Ramelot, A. Eletsky, T. Szyperski, M.A. Kennedy, J. Prestegard, G.T. Montelione, D. Baker, NMR structure determination for larger proteins using backbone-only data. Science, 2010, 327, 1014–1018.</ref>, NOE distance restraints<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>, and pseudocontact chemical shifts (PCS)<ref>C. Schmitz, R. Vernon, G. Otting, D. Baker, T. Huber, Protein structure determination from pseudocontact shifts using ROSETTA. Journal of molecular biology, 2012, 416, 668–677.</ref>. The original CS-Rosetta protocol was based on a combination of ROSETTAs de-novo structure prediction protocol featuring Monte-Carlo assembly of molecular fragments and subsequent full-atom relax. Later an iterative protocol for '''R'''esolution '''A'''dapted '''S'''tructural '''Rec'''ombination ('''RASREC''') was developed and shown to significantly extend the convergence of CS-ROSETTA towards larger structures. A combination of RASREC and sparse NOE distance restraints from ILV-labelled proteins was shown to allow accurate 3D structure determination for proteins up to 40kDa<ref>O.F. Lange, P. Rossi, N. G. Sgourakis, Y. Song, H. Lee, J. M. Aramini, A. Eretekin, R. Xiao, T. B. Acton, G. T. Montelione, and David Baker, <i>P. Natl. Acad. Sci. USA</i> EE (2012), 1-6</ref>.

	The software is freely available for academic use and can be licensed for commercial use ([http://www.csrosetta.org/installation installation guide]). A software [http://www.csrosetta.org/manual manual] and [http://www.csrosetta.org/tutorials tutorials] are provided on the supporting website [http://www.csrosetta.org www.csrosetta.org].		The software is freely available for academic use and can be licensed for commercial use ([http://www.csrosetta.org/installation installation guide]). A software [http://www.csrosetta.org/manual manual] and [http://www.csrosetta.org/tutorials tutorials] are provided on the supporting website [http://www.csrosetta.org www.csrosetta.org].