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.