Structure Calculation Using AS-DP - Revision history

Jma at 21:38, 6 January 2010

2010-01-06T21:38:06Z

← Older revision		Revision as of 21:38, 6 January 2010
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	== '''Theory''' ==		== '''Theory''' ==

	Recently, we have developed an improved version of AutoStructure - AS-DP. The new feature of AS-DP is using DP scores from RPF software to select models generated in AutoStructure’s iterative cycles. Only the top models with highest DP scores and lowest target function (CYANA) or conformational energy (XPLOR) values are selected for iterative AutoStructure NOE analysis. Using a DP filter for model selection improves the accuracy of the selected intermediate structures for iterative NOE analysis and therefore improves the accuracy of NOESY crosspeak assignments and final models. AS-DP has been successfully assessed in the first CASD-NMR workshop ~~(Ref.~~ 1) in May 2009.		Recently, we have developed an improved version of AutoStructure - AS-DP. The new feature of AS-DP is using DP scores from RPF software to select models generated in AutoStructure’s iterative cycles. Only the top models with highest DP scores and lowest target function (CYANA) or conformational energy (XPLOR) values are selected for iterative AutoStructure NOE analysis. Using a DP filter for model selection improves the accuracy of the selected intermediate structures for iterative NOE analysis and therefore improves the accuracy of NOESY crosspeak assignments and final models. AS-DP has been successfully assessed in the first CASD-NMR workshop [1] in May 2009.

	== '''Using AS-DP''' ==		== '''Using AS-DP''' ==
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	== '''References'''<br> ==		== '''References'''<br> ==

	1.    Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J.F., Giachetti, A., Guerry, P., Guntert, P., Herrmann, T., Huang, Y.J., Jonker, H.R.A., Mao, B., Malliavin, T.E., Montelione, G.T., Nilges, M., Raman, S., Schot, G., Vranken, W.F., Vuister, G.W., and Bonvin, A.M.J.J. (2009) CASD-NMR: a rolling experiment for the critical assessment of automated structure determination of proteins from NMR data. ''Nature Methods 6'', 625-6.		[http://www.ncbi.nlm.nih.gov/pubmed/19718014?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=3 1.    Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J.F., Giachetti, A., Guerry, P., Guntert, P., Herrmann, T., Huang, Y.J., Jonker, H.R.A., Mao, B., Malliavin, T.E., Montelione, G.T., Nilges, M., Raman, S., Schot, G., Vranken, W.F., Vuister, G.W., and Bonvin, A.M.J.J. (2009) CASD-NMR: a rolling experiment for the critical assessment of automated structure determination of proteins from NMR data. ''Nature Methods 6'', 625-6.]

	<br>		<br>

	~~-- JanetHuang/JimAramini - 09 Nov 2009~~

Jma at 01:16, 10 November 2009

2009-11-10T01:16:49Z

← Older revision		Revision as of 01:16, 10 November 2009
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	Recently, we have developed an improved version of AutoStructure - AS-DP. The new feature of AS-DP is using DP scores from RPF software to select models generated in AutoStructure’s iterative cycles. Only the top models with highest DP scores and lowest target function (CYANA) or conformational energy (XPLOR) values are selected for iterative AutoStructure NOE analysis. Using a DP filter for model selection improves the accuracy of the selected intermediate structures for iterative NOE analysis and therefore improves the accuracy of NOESY crosspeak assignments and final models. AS-DP has been successfully assessed in the first CASD-NMR workshop (Ref. 1) in May 2009.		Recently, we have developed an improved version of AutoStructure - AS-DP. The new feature of AS-DP is using DP scores from RPF software to select models generated in AutoStructure’s iterative cycles. Only the top models with highest DP scores and lowest target function (CYANA) or conformational energy (XPLOR) values are selected for iterative AutoStructure NOE analysis. Using a DP filter for model selection improves the accuracy of the selected intermediate structures for iterative NOE analysis and therefore improves the accuracy of NOESY crosspeak assignments and final models. AS-DP has been successfully assessed in the first CASD-NMR workshop (Ref. 1) in May 2009.

	== '''Using AS-DP''' ==		== '''Using AS-DP''' ==

	A new version of AutoStructure featuring the AS-DP capability is due to be released in 2010.		A new version of AutoStructure featuring the AS-DP capability is due to be released in 2010.

	'''References''' ==		== '''References'''<br> ==

	1.    Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J.F., Giachetti, A., Guerry, P., Guntert, P., Herrmann, T., Huang, Y.J., Jonker, H.R.A., Mao, B., Malliavin, T.E., Montelione, G.T., Nilges, M., Raman, S., Schot, G., Vranken, W.F., Vuister, G.W., and Bonvin, A.M.J.J. (2009) CASD-NMR: a rolling experiment for the critical assessment of automated structure determination of proteins from NMR data. ''Nature Methods 6'', 625-6.

			1.    Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J.F., Giachetti, A., Guerry, P., Guntert, P., Herrmann, T., Huang, Y.J., Jonker, H.R.A., Mao, B., Malliavin, T.E., Montelione, G.T., Nilges, M., Raman, S., Schot, G., Vranken, W.F., Vuister, G.W., and Bonvin, A.M.J.J. (2009) CASD-NMR: a rolling experiment for the critical assessment of automated structure determination of proteins from NMR data. ''Nature Methods 6'', 625-6.

			<br>

	-- JanetHuang/JimAramini - 09 Nov 2009		-- JanetHuang/JimAramini - 09 Nov 2009

Jma: Created page with '== '''Theory''' == Recently, we have developed an improved version of AutoStructure - AS-DP. The new feature of AS-DP is using DP scores from RPF software to select models gener…'

2009-11-10T01:15:05Z

Created page with '== '''Theory''' == Recently, we have developed an improved version of AutoStructure - AS-DP. The new feature of AS-DP is using DP scores from RPF software to select models gener…'

New page

== '''Theory''' ==

Recently, we have developed an improved version of AutoStructure - AS-DP. The new feature of AS-DP is using DP scores from RPF software to select models generated in AutoStructure’s iterative cycles. Only the top models with highest DP scores and lowest target function (CYANA) or conformational energy (XPLOR) values are selected for iterative AutoStructure NOE analysis. Using a DP filter for model selection improves the accuracy of the selected intermediate structures for iterative NOE analysis and therefore improves the accuracy of NOESY crosspeak assignments and final models. AS-DP has been successfully assessed in the first CASD-NMR workshop (Ref. 1) in May 2009.

== '''Using AS-DP''' ==

A new version of AutoStructure featuring the AS-DP capability is due to be released in 2010.

'''References''' ==

1.    Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J.F., Giachetti, A., Guerry, P., Guntert, P., Herrmann, T., Huang, Y.J., Jonker, H.R.A., Mao, B., Malliavin, T.E., Montelione, G.T., Nilges, M., Raman, S., Schot, G., Vranken, W.F., Vuister, G.W., and Bonvin, A.M.J.J. (2009) CASD-NMR: a rolling experiment for the critical assessment of automated structure determination of proteins from NMR data. ''Nature Methods 6'', 625-6.

-- JanetHuang/JimAramini - 09 Nov 2009