In-house software
08/08/24 13:30
A number of useful in-house programs have been produced that are available for download. Programs are either in C++ (making frequent use of the GSL), python (2.7, usually requiring numpy, scipy, matplotlib and nmrGlue modules) or a mixture of both. Outputs are produced in either gnuplot, matplotlib or latex. For programs with graphical user interfaces, wx-python will be required. Specific installation instructions and requirements are described for each program individually.
uSTA
06/08/24 16:19
Software for analysing saturation transfer difference NMR data. The uSTA workflow takes FIDs, processes the data (using nmrPipe), and runs the in-built unidecNMR peak picker on the data and creates a heat map showing the ligand binding pose in the complex. Combined with data varying the protein/ligand concentration and ratio, an analysis routine is provided that returns Kds/Kon/Koff via Bloch-McConnell matrix analysis.
The manuscript is here https://www.science.org/doi/10.1126/science.abm3125
Download the software HERE.
The manuscript is here https://www.science.org/doi/10.1126/science.abm3125
Download the software HERE.
Seedless
06/08/24 16:17
NMR experiments require sequences of radio frequency (RF) ‘pulses’ to manipulate nuclear spins. Signal is lost due to non-uniform excitation of nuclear spins resonating at different energies (chemical shifts) and inhomogeneity in the RF unavoidably generated by hardware over the sample volume. To overcome this, we present Seedless, a tool to calculate NMR pulses that compensate for these effects to enhance control of magnetisation and boost signal. As calculations take only a few seconds using an optimised GRadient Ascent Pulse Engineering (GRAPE) implementation, this now allows pulses to be generated ‘on-the-fly’, optimised for individual samples and spectrometers. Each calculated pulse requires bands of chemical shift to be identified, over which one of 4 transforms will be performed, selected from a set that covers all commonly used applications: a universal rotation (e.g. 90o about the x axis), including as a special case an identity operation (return spins in the same state as theystarted), state-to-state (e.g. Z->Y), an XYcite (Z->XY plane), or a novel type, a suppression, that leaves spins minimally perturbed at all times during the pulse. Using imaging experiments we demonstrate our pulses effectively both increase the size of the coil volume and signal-to-noise in all experiments. We illustrate the approach by devising ultra-broadband pulses (300 ppm excitation pulse for 19F 1D spectra), a 15N HSQC with 58% increased S/N (950 MHz spectrometer + cryoprobe), triple resonance biomolecular NMR experiments such as HNCACO with 55% increased S/N (600 MHz spectrometer + RT probe), and a highly efficient pulse sequence for water suppression. The 8 optimised pulse sequences presented required 54 bespoke pulses all calculated on-the-fly. Seedless provides a means to enhance sensitivity in all pulse sequences in a manner that can be tailored to all samples/hardware being used.
The manuscript is currently under review but you are welcome test this and please provide feedback!
Download Seedless HERE.
The manuscript is currently under review but you are welcome test this and please provide feedback!
Download Seedless HERE.
Magma
06/07/24 16:22
MAGMA is software for assigning methyl resonances using through space NMR data (e.g NOE for solution-state or DREAM for solid-state) using a known structure of a protein. The algorithm uses graph theory to perform an exact search of all possible assignment solutions, returning a result that should include all possible assignments each given residue, given the supplied NOEs. Accuracy on the benchmark is very high: we have a 100% success rate in confident (1 option assignments) in giving the correct assignment in our benchmark.
Details can be found in 'Pritisanac et al. JACS 2017' DOI: 10.1021/jacs.6b11358.
Download the Software HERE.
Details can be found in 'Pritisanac et al. JACS 2017' DOI: 10.1021/jacs.6b11358.
Download the Software HERE.
unidecNMR
06/06/24 16:22
To extract information from NMR experiments, users need to identify the number of resonances in the spectrum, together with characteristic features such as chemical shifts and intensities. In many applications, particularly those involving biomolecules, this procedure is typically a manual and laborious process. While many algorithms are available to tackle this problem, their performance tends to be inferior to that of an experienced user. Here, we introduce UnidecNMR, which identifies resonances in NMR spectra using deconvolution. We demonstrate its favourable performance on 1 and 2D simulated spectra, strongly overlapped 1D spectra of oligosaccharides and 2D HSQC, 3D HNCO, 3D HNCA and 3/4D methyl-methyl NOE experimental spectra from a range of proteins. UnidecNMR outperforms a number of freely available algorithms and provides results that are either of similar quality to those generated manually, or in the case of NOE data, superior. We demonstrate that introducing additional restraints, such as a 2D peak list when analysing 3 and 4D data and incorporating reflection symmetry in NOE analysis further improves the results. UnidecNMR outputs a back-calculated spectrum and a peak list, both of which can be easily examined using the supplied GUI. The software allows interactive processing of raw data using nmrPipe. UnidecNMR is free for academic use and can function as either part of an automatic pipeline or provide an excellent ‘first guess’ of peak locations as part of a semi-automatic analysis.
Paper under review.
Download the software HERE.
Paper under review.
Download the software HERE.