Overview
PINE-SPARKY is the original NMRFAM plugin built to verify probabilistic PINE assignments inside Sparky. It imports the backbone and sidechain resonance assignments returned by the PINE server directly into the spectra and color-codes them by confidence, so a spectroscopist can visually review and correct automated assignments without leaving the program. Plugins described in PINE-SPARKY are also available in POKY.
PINE-SPARKY was developed at NMRFAM by Prof. Woonghee Lee and described in Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL. "PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy." Bioinformatics, 2009;25(16):2085–2087 — see the Publications page.
How it works
After peaks are assigned by I-PINE webserver, returned backbone (and optionally sidechain) chemical shift assignments along with a confidence probability are converted these into peak assignments and color-codes the assignment labels by confidence, letting you immediately spot residues that need manual attention versus assignments that are reliable as-is.
PINE-SPARKY.2
PINE-SPARKY.2 was also developed by Prof. Woonghee Lee. Where the original PINE-SPARKY focuses on verifying assignments PINE has already returned, PINE-SPARKY.2's job is the other half of the workflow: making the submission to the Enhanced I-PINE server and the import of its results a few mouse clicks, directly from the POKY interface — plus pre-assignment restraints, selective residue-type labeling, and one-click CS-Rosetta structure calculation from the same PINE results. See Automatic Assignment for how PINE-SPARKY.2 fits into POKY's current assignment tools.