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ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) is a fully automated method that integrates protein NMR data collection, chemical shift assignment, and secondary structure determination. ADAPT-NMR supervises the collection of data from tilted 2Dplanes from a variety of 3D double- and triple-resonance 3D experiments. Data collection proceeds until the desired level of assignment is achieved or until additional data fail to improve the level of assignment. Because traditional assignment packages, such as SPARKY, NMRVIEW, CARA and CCPNmr, are not designed to make assignments from tilted 2D planes data, we have developed this tool for evaluating and extending the results from ADAPT-NMR.

ADAPT-NMR Enhancer is a tool for visualizing the tilted 2D plane data from ADAPT-NMR, for correlating peaks in the tilted planes with peaks in the reconstituted 3D spectrum, and for tracing the assignments of these peaks to atoms in the covalent structure of the protein.

ADAPT-NMR Enhancer can be used in the following three ways:
    1. To visualize peaks in 2D tilted planes from specific 3D NMR experiments and to correlate these with corresponding peaks in 3D space. The peaks picked by ADAPT-NMR are shown, and these can be un-picked and additional peaks can be picked.
ADAPT-NMR Enhancer can display up to six tilted 2D spectra along with the picked peaks. This enables the user to evaluate the quality of the automated peak picking and assignment by ADAPT-NMR. Peaks in 3D space are easily correlated with evidence for their existence in tilted 2D planes. Users add and remove peaks manually and in doing so modify or refine assignments.
    2. To create a modified peak list as input to an ADAPT-NMR assignment iteration.
The visualization and verification tools offered by ADAPT-NMR Enhancer enable the user to pick additional peaks, delete noise peaks, and separate overlapped peaks. The refined peak list can then be submitted to ADAPT-NMR for probabilistic assignment.
    3. To complete resonance assignments with a manual interface.
If the user wishes to improve the number or confidence level of the assignments over those achieved following peak list refinement and submission to ADAPT-NMR, the PINE-SPARKY-like tools supported by ADAPT-NMR Enhancer support the verification and extension of assignments by an atom-by-atom and peak-by-peak approach.


ADAPT-NMR Enhancer

Please cite:
Lee W, Bahrami A, Markley JL.
ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy.
Bioinformatics. 2013 Feb 15;29(4):515-7. doi: 10.1093/bioinformatics/bts692. Epub 2012 Dec 7.

Last Updated: June 18, 2013
By Woonghee Lee (whlee@nmrfam.wisc.edu)


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