Deep Picker: a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra

STEP 1: Time domain spectra processing
Your name and institute*: User chosen experimental name (optional):

HSQC spectrum (required)

HSQC fid file (required, usually called fid or ser):
acqus file (required, usually called acqus):
acqus2 file (required, usually called acqu2s):
pseudo-3D acquistion squence
Negative imaginary data (indirect dimension)?

Bruker fid data format information

You can find raw fid data in the experimental folder, such as your_exp_name/2, where 2 is EXP ID. The file is usually named fid (or ser)
The acquisition status file is usually called acqus (not acqu) in the same folder as the FID data file.
You can also drag and drop fid and/or acqus file, or their parent folder to the box above.
The server will run automatic phase correction, after ZF and FF.

Spectrum processing requirements, please read carefully.

The number of points per peak (PPP), which is given by the number of data points that sample the peak’s full width at half height (FWHH), is allowed to vary either from 6 to 20 (optimal: 12) points or from 4 to 12 (optimal: 8) points. This requirement can be fulfilled easily by applying proper fold of zero filling. Typically, 4 to 8 times ( -zf 2 or 3 in nmrPipe ) of zero-filling is required to reach these PPPs.
Please use the 2PI-Kaiser window function for apodization in the NMRPipe software with the command “SP -off 0.5 -end 0.896 -pow 3.684”. The resulting peak shapes can then be modeled in all dimensions with good accuracy using a Voigt profile that combines variable amounts of Lorentzian vs. Gaussian character.
When you adjust lowest contour level, peaks that are fall below it will become invisible. However, all peaks will be kept in the downloaded file.

STEP2: Peak picking and peak fitting

Peak fitting is recommended only if compound quantification is planed. It may take up to several hours for a complex spectrum

Noise level Drawing
Lowest contour level Logarithmic scale
Lowest contour level Logarithmic scale
Current contour level cutoff: 1
Current contour level cutoff: 1
Control: Brush an area to Zoom in, or remove peaks within this area. , ,

Download section

Reference

Da-Wei Li, Alex Hansen, Lei Bruschweiler-Li, Chunhua Yuan and Rafael Brüschweiler; DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra; natural communication; Article number: 5229 (2021);

Questions or comments? Please feel free to contact us.

Acknowledgement

This web server and the research that led to it is supported by the National Institutes of Health (Grant R01 GM 066041).
Most chemical shifts in COLMAR database were retrieved from the existing databases listed below, which all allow public access.

*This information is only used for the compilation of our webserver usage data.

This server is last updated at September 16 2024 06:45:50.