Resonance Assignment/The PINE Server - Revision history

Jlmills at 15:34, 27 April 2010

2010-04-27T15:34:00Z

Agutmana: moved The PINE Server to Resonance Assignment/The PINE Server

2010-01-06T00:15:59Z

moved The PINE Server to Resonance Assignment/The PINE Server

← Older revision	Revision as of 00:15, 6 January 2010
(No difference)

Jma at 22:34, 10 November 2009

2009-11-10T22:34:55Z

← Older revision		Revision as of 22:34, 10 November 2009
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	==== Figure 1:  The PINE Server ====		==== Figure 1:  The PINE Server ====

	[[Image:PINEserver.png]]<br>		[[Image:PINEserver.png]]<br>

	=== '''PINE Output''' ===		=== '''PINE Output''' ===

			The user is e-mailed a list of PINE results files, as well as a zip file for download containing the entire output (Figure 2).

			The PINE output files include:

			*pecan_figure.jpg:  shows the predicted secondary structure elements across the sequence
			*protein.jpg:  a small figure showing the completeness of the assignment across the sequence
			*protein.pis:  a text file showing the assignments and percent confidences over the entire sequence.  This is particularly useful to study for any missing assignments.
			*the assignments in BMRB format
			*assigned peak lists in Sparky format

			==== Figure 2:  PINE Results ====

			[[Image:PINEresults.png]]

	== '''References''' ==		== '''References''' ==

	1.    Bahrami, A., Assadi, A.H., Markley, J.L.  and Eghbalnia, H.R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. ''PLoS Comput. Biol. 5'', e1000307.		1.    Bahrami, A., Assadi, A.H., Markley, J.L.  and Eghbalnia, H.R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. ''PLoS Comput. Biol. 5'', e1000307.

Jma at 15:23, 10 November 2009

2009-11-10T15:23:09Z

← Older revision		Revision as of 15:23, 10 November 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

	The ~~recently developed~~ PINE program (Probablistic Interaction Network of Evidence) uses a novel aglorithm for the automated assignment of both backbone and side chain protein NMR resonances (Ref. 1).  PINE is available from a freely accessible [http://miranda.nmrfam.wisc.edu/PINE/ web server]. It is reported to have > 90% accuracy for backbone resonances and > 80% for aliphatic side chain resonances.		The PINE program (Probablistic Interaction Network of Evidence), recently developed by Arash Bahrami (NMRFAM, U. of Wisconsin), uses a novel aglorithm for the automated assignment of both backbone and side chain protein NMR resonances (Ref. 1).  PINE is available from a freely accessible [http://miranda.nmrfam.wisc.edu/PINE/ web server]. It is reported to have > 90% accuracy for backbone resonances and > 80% for aliphatic side chain resonances.

	== '''Using the PINE Server''' ==		== '''Using the PINE Server''' ==

	=== '''Input Files''' ===		=== '''Input Files''' ===

	*amino acid sequence of the protein target either in single-letter or three-letter format.		*amino acid sequence of the protein target either in single-letter or three-letter format.
	*spectral peak lists.  The program can accept peak lists in several formats including:		*spectral peak lists.  The program can accept peak lists in several formats including:
	*SPARKY		*SPARKY
	*XEASY		*XEASY
	*PINE		*PINE
	*additional information including:		*additional information including:
	*pre-assigned resonances		*pre-assigned resonances
	*amino acid selective labelling information		*amino acid selective labelling information
	*grouped spins systems		*grouped spins systems

			<br>

			=== The PINE Server ===

	~~===~~ The PINE ~~Server ===~~		The PINE server is relatively simple to use (Figure 1).  The user uploads the protein sequence, spectral peak lists and any additional information and simply submits to the server.  There are extensive help links for the user on this main page.  Note that for Sparky peak lists, the current version of the server (1.0) cannot tolerate the Notes column; so, remove this column prior to submission.  The server returns the results by e-mail normally within a few minutes.  If you have a problem, [mailto:mani@nmrfam.wisc.edu e-mail] the Mani team.<br>

	~~The PINE server is relatively simple to use (~~Figure 1).  The user uploads the protein sequence, spectral peak lists and any additional information and simply submits to the server.  There are extensive help links for the user on this main page.  Note that for Sparjy peak lists, the current version of the server (1.0) cannot tolerate the Notes column; so, remove this column prior to submission.		==== Figure 1:  The PINE Server ====

	~~==== Figure 1~~:~~  The PINE Server ====~~		[[Image:PINEserver.png]]<br>

	~~[[Image:PINEserver.png]]~~		=== '''PINE Output''' ===
	===

	~~=== '''PINE Output''' ===~~


			== '''References''' ==


	== '''References''' ==

	1.    Bahrami, A., Assadi, A.H., Markley, J.L.  and Eghbalnia, H.R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. ''PLoS Comput. Biol. 5'', e1000307.		1.    Bahrami, A., Assadi, A.H., Markley, J.L.  and Eghbalnia, H.R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. ''PLoS Comput. Biol. 5'', e1000307.

Jma: Created page with '== '''Introduction''' == The recently developed PINE program (Probablistic Interaction Network of Evidence) uses a novel aglorithm for the automated assignment of both back…'

2009-11-10T15:02:05Z

Created page with '== '''Introduction''' == The recently developed PINE program (Probablistic Interaction Network of Evidence) uses a novel aglorithm for the automated assignment of both back…'

New page

== '''Introduction''' ==

The recently developed PINE program (Probablistic Interaction Network of Evidence) uses a novel aglorithm for the automated assignment of both backbone and side chain protein NMR resonances (Ref. 1).  PINE is available from a freely accessible [http://miranda.nmrfam.wisc.edu/PINE/ web server]. It is reported to have > 90% accuracy for backbone resonances and > 80% for aliphatic side chain resonances.

== '''Using the PINE Server''' ==

=== '''Input Files''' ===

*amino acid sequence of the protein target either in single-letter or three-letter format.
*spectral peak lists.  The program can accept peak lists in several formats including:
*SPARKY
*XEASY
*PINE
*additional information including:
*pre-assigned resonances
*amino acid selective labelling information
*grouped spins systems

=== The PINE Server ===

The PINE server is relatively simple to use (Figure 1).  The user uploads the protein sequence, spectral peak lists and any additional information and simply submits to the server.  There are extensive help links for the user on this main page.  Note that for Sparjy peak lists, the current version of the server (1.0) cannot tolerate the Notes column; so, remove this column prior to submission.

==== Figure 1:  The PINE Server ====

[[Image:PINEserver.png]]
===

=== '''PINE Output''' ===

== '''References''' ==

1.    Bahrami, A., Assadi, A.H., Markley, J.L.  and Eghbalnia, H.R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. ''PLoS Comput. Biol. 5'', e1000307.

← Older revision		Revision as of 15:34, 27 April 2010
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	The PINE program (Probablistic Interaction Network of Evidence), recently developed by Arash Bahrami (NMRFAM, U. of Wisconsin), uses a novel aglorithm for the automated assignment of both backbone and side chain protein NMR resonances (Ref. 1).  PINE is available from a freely accessible [http://~~miranda~~.nmrfam.wisc.edu~~/PINE~~/ web server]. It is reported to have > 90% accuracy for backbone resonances and > 80% for aliphatic side chain resonances.		The PINE program (Probablistic Interaction Network of Evidence), recently developed by Arash Bahrami (NMRFAM, U. of Wisconsin), uses a novel aglorithm for the automated assignment of both backbone and side chain protein NMR resonances (Ref. 1).  PINE is available from a freely accessible [http://pine.nmrfam.wisc.edu/ web server]. It is reported to have > 90% accuracy for backbone resonances and > 80% for aliphatic side chain resonances.

	== '''Using the PINE Server''' ==		== '''Using the PINE Server''' ==
Line 29:		Line 29:
	=== '''PINE Output''' ===		=== '''PINE Output''' ===

	The user is e-mailed a list of PINE results files, as well as a zip file for download containing the entire output (Figure 2).		The user is e-mailed a list of PINE results files, as well as a zip file for download containing the entire output (Figure 2).

	The PINE output files include:		The PINE output files include:

	*pecan_figure.jpg:  shows the predicted secondary structure elements across the sequence		*pecan_figure.jpg:  shows the predicted secondary structure elements across the sequence
	*protein.jpg:  a small figure showing the completeness of the assignment across the sequence		*protein.jpg:  a small figure showing the completeness of the assignment across the sequence
	*protein.pis:  a text file showing the assignments and percent confidences over the entire sequence.  This is particularly useful to study for any missing assignments.		*protein.pis:  a text file showing the assignments and percent confidences over the entire sequence.  This is particularly useful to study for any missing assignments.
	*the assignments in BMRB format		*the assignments in BMRB format
	*assigned peak lists in Sparky format		*assigned peak lists in Sparky format

	==== Figure 2:  PINE Results ====		==== Figure 2:  PINE Results ====

	[[Image:PINEresults.png]]		[[Image:PINEresults.png]]

	== '''References''' ==		== '''References''' ==

	1.    Bahrami, A., Assadi, A.H., Markley, J.L.  and Eghbalnia, H.R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. ''PLoS Comput. Biol. 5'', e1000307.		1.    Bahrami, A., Assadi, A.H., Markley, J.L.  and Eghbalnia, H.R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. ''PLoS Comput. Biol. 5'', e1000307.