Mani Tools - PINE Server

PINE Server v.2.0

Bahrami, A., Assadi, A., Markley, J. L. & Eghbalnia, H., Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak lists from Protein NMR Spectroscopy, PLoS Comput Biol. 2009 Mar;5(3):e1000307. (read)

We are running PINE v.3.0b in parallel. Please note that this version is much more accurate than PINE v.2.0, however, as it is on beta-stage, any bug reports are welcomed. [bug report] New experiments (HNHAHB, TOCSY-HSQC, HN(CA)NNH, N15-NOESY) and 3D coordinates are newly added in the new version. Please click here to try them since this web page does not support newly supported data.

PINE accepts, as input, the sequence of the protein plus peak lists (or spin systems) from a variety of NMR experiments and offers automatic backbone and sidechain assignments, detection and automated correction of potential referencing problems or inconsistent assignments and secondary structure determination.

• Acceptable formats for input data are

1) Amino acid sequences and peak lists in Sparky format, XEASY format, or PINE simple format. Sample files and brief instructions are available here.

2) If you have already analyzed the spin systems, you can upload your spin system file in correct format in the spin system field at the end of the webpage. In that case please do NOT upload peak lists, however you still need to upload the sequence file in correct format.

• PINE also offers assignments for proteins that have been selectively labeled or have prior partial assignments.
• Instruction for PINE output files can also be found here.
• Assignment results, including secondary structure identification, are returned via email.
• Depending on the size of the protein, the quality of input data, and number of current jobs, run times vary from a few minutes to a few hours.
• Please checkout our visual assignment tool PINE-SPARKY for verification of PINE automated assignments. It is already pre-installed in NMRFAM-SPARKY, the enhanced version of a long-time favorite, UCSF-SPARKY. (download link). You can also submit a job and import results from NMRFAM-SPARKY without visiting this webpage by using PINE-SPARKY.2 plugin. (PINE-SPARKY.2)

  
  Lee, W., Westler, W. M., Bahrami, A., Markley, J. L., PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinformatics. 2009 Aug 15;25(16):2085-7. (read)

  Lee, W., Tonelli, M., Markley, J. L., NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2015 Apr 15;31(8):1325-7. (read)

  Lee, W., Cornilescu, G., Dashti, H., Eghbalnia, H. R., Tonelli, M., Westler, W. M., Butcher, S. E., Henzler-Wildman, K. A., Markley, J. L., Integrative NMR for biomolecular research. J Biomol NMR. 2016 Apr;64(4):307-32. (read)

This service offered by the National Magnetic Resonance Facility at Madison. Updated Sep 2017.

OPTIONAL: Prot_file, Pre-assignment, Selective_Labeling, Spin_Systems

Upload the empty Prot_file IF you want the output in Xeasy format (peak assigned according to prot file numbers). (Sample)

Upload the Pre-assignment file in BMRB format if any pre-assignment is available. DO NOT UPLOAD IF THE FILE IS EMPTY. (Instruction)

Upload the Selective_Labeling information file if available. (Instruction)

Upload your Spin_Systems here if you already made spin systems. Do NOT upload spin systems and peak lists together! (Instruction)