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Woonghee Lee, Arash Bahrami, Hesam Dashti, Hamid R. Eghbalnia, Marco Tonelli, William M. Westler, John L. Markley. (2019) Journal of Biomolecular NMR. 73(5): 213-222. [click to read]

This is the I-PINE web server. Please let us know any unexpected behavior from this server. You can also use PINE from here.

I-PINE accepts, as input, the sequence of the protein plus peak lists (or spin systems) from a variety of NMR experiments and offers automated backbone and sidechain assignments, detection and automated correction of potential referencing problems or inconsistent assignments, secondary structure determination, 3D structure prediction, cysteine oxidation, proline isomerization and hydrophobic core detection.

Most jobs take only a few minutes. The results will be accessible from provided URL and job identification number and also sent to the user via email (optional). If you do not receive any email including spam folder longer than a few hours, please contact NMRFAM.

I-PINE supports more types of input NMR data than its precursor PINE including from three- and four-dimensional NOE experiments, achieves more accurate and complete chemical shift assignments, and supports more comprehensive visualization of chemical shift based analysis of protein structure and dynamics. Users of the I-PINE web server can not only submit unassigned peak lists or spin systems but also sets of previously assigned chemical shifts as inputs. The output of I-PINE is available in formats used as input by other software packages. A user can choose one of three interfaces when submitting a job to the I-PINE web server (http://i-pine.nmrfam.wisc.edu): a CLI (command-line user interface) with a versatile python script pyIPINE.py, a GUI (graphical user interface) with the PINE-SPARKY.2 plugin of the popular NMR analysis software package NMRFAM-SPARKY, or a WUI (web-based user interface). A single submission to I-PINE automatically achieves what previously required multiple tedious discrete tasks. Submitted data are kept confidential and are not viewable by others. Complete output information is available in a custom-built web page, which is accessible from the job identification number.

Required input files to run I-PINE are,

Optional input files to enhance I-PINE are,

Please note that we developed PINE-SPARKY.2 plug-in to run and import I-PINE easy in the NMRFAM-SPARKY program. Verifying results from I-PINE is always necessary because assignment quality is dependent on user inputs, which are often incomplete for many reasons. We provide PINE-SPARKY extensions (two-letter-code ab, pp, pr) for visual verification of PINE results in the NMRFAM-SPARKY program. I-PINE is a part of Integrative NMR research platform, which makes biomolecular NMR spectroscopy much more accessible by integrating software tools so that they interact efficiently in ways that support both manual and automated approaches, result validation, and data visualization. Our open access publication of Integrative NMR is available.