Dear MDDNMR users,
We like to announce a set of examples designed for comparing performance of several popular NUS processing methods from the MDDNMR package and other programs:
MDD [1], IRLS [2], IST [2], LR [3], hmsIST [4], NESTA [5], SCRUB [6] and SMILE [7].
We start with representative protein spectra 2D HSQC, 2D NOESY, 3D 1H-15N NOESY-HSQC, and 3D HNCO, recorded in full.
MDDNMR allows to sparsify full spectra for a given NUS schedule. All algorithms use exactly the same input and output in nmrPipe format.
Thus a fair comparison of different algorithms and NUS schemes in respect to the reconstructed spectra quality is possible.
We are looking for repeating the procedure for many sampling schedules to make the analysis more representative.
However, we like to make the scripts and examples public as soon as possible in order to allow the discussion and independent testing.
The processing script and analysis used in the examples are general and can be used for comparisons using any other full spectrum.
For the processing, the scripts use default/recommended parameters.
You can look at (e.g. in nmrDraw) and compare the reconstructed spectra with the reference and between different algorithms.
In addition, there is a simple analysis of the spectra quality.
Namely, intensities of the peaks defined in the nmrPipe peak lists are compared in the reference and reconstructed spectra.
The correlation plots and correlation coefficients are displayed in gnuplot.
In order to process the spectra and look at the comparisons results you need
- Install nmrPipe, MDDNMR, and other the programs.
- MDDNMR IRLS, IST, MDD, nus-FT: http://mddnmr.spektrino.com
- SMILE: https://spin.niddk.nih.gov/bax/software/SMILE/
- SCRUB: https://coggins.biochem.duke.edu/scrub/
- NESTA: http://nestanmr.com/
- hmsIST: http://gwagner.med.harvard.edu/intranet/hmsIST/
- Download example spectra from
here
- Download processing/analysis scripts from here
- In the processing directories for individual spectra, set correct path to the programs in the headers of main processing scripts *.sh .
You may the skip processing for some algorithms, by setting the corresponding path variable to a nonexistent name
-
V. Y. Orekhov, V. A. Jaravine, Prog Nucl Mag Res Sp 2011, 59, 271-292.
-
K. Kazimierczuk, V. Y. Orekhov, Angew. Chem.-Int. Edit. 2011, 50, 5556-
5559.
-
X. B. Qu, M. Mayzel, J. F. Cai, Z. Chen, V. Orekhov, Angew Chem Int Edit
2015, 54, 852-854.
-
S. G. Hyberts, A. G. Milbradt, A. B. Wagner, H. Arthanari, G. Wagner, J.
Biomol. NMR 2012, 52, 315-327.
-
S. J. Sun, M. Gill, Y. F. Li, M. Huang, R. A. Byrd, J. Biomol. NMR 2015, 62,
105-117.
-
B. E. Coggins, J. W. Werner-Allen, A. Yan, P. Zhou, J. Am. Chem. Soc. 2012,
134, 18619-18630.
-
J. Ying, F. Delaglio, D. A. Torchia, A. Bax, J Biomol NMR 2016, 1-18.
- Install nmrPipe, MDDNMR, and other the programs.
- MDDNMR IRLS, IST, MDD, nus-FT: http://mddnmr.spektrino.com
- SMILE: https://spin.niddk.nih.gov/bax/software/SMILE/
- SCRUB: https://coggins.biochem.duke.edu/scrub/
- NESTA: http://nestanmr.com/
- hmsIST: http://gwagner.med.harvard.edu/intranet/hmsIST/
- Download example spectra from here
- Download processing/analysis scripts from here
- In the processing directories for individual spectra, set correct path to the programs in the headers of main processing scripts *.sh . You may the skip processing for some algorithms, by setting the corresponding path variable to a nonexistent name
- V. Y. Orekhov, V. A. Jaravine, Prog Nucl Mag Res Sp 2011, 59, 271-292.
- K. Kazimierczuk, V. Y. Orekhov, Angew. Chem.-Int. Edit. 2011, 50, 5556- 5559.
- X. B. Qu, M. Mayzel, J. F. Cai, Z. Chen, V. Orekhov, Angew Chem Int Edit 2015, 54, 852-854.
- S. G. Hyberts, A. G. Milbradt, A. B. Wagner, H. Arthanari, G. Wagner, J. Biomol. NMR 2012, 52, 315-327.
- S. J. Sun, M. Gill, Y. F. Li, M. Huang, R. A. Byrd, J. Biomol. NMR 2015, 62, 105-117.
- B. E. Coggins, J. W. Werner-Allen, A. Yan, P. Zhou, J. Am. Chem. Soc. 2012, 134, 18619-18630.
- J. Ying, F. Delaglio, D. A. Torchia, A. Bax, J Biomol NMR 2016, 1-18.