Resonance Assignment/The PINE Server: Difference between revisions
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== '''Introduction''' == | == '''Introduction''' == | ||
The | 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 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> | |||
==== Figure 1: The PINE Server ==== | |||
[[Image:PINEserver.png]]<br> | |||
=== '''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. | ||
Revision as of 15:23, 10 November 2009
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 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 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, e-mail the Mani team.
Figure 1: The PINE Server
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.