Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra

Paramagnetic metal ions with fast-relaxing electrons generate pseudocontact shifts (PCSs), residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) and cross-correlated relaxation (CCR) in the nuclear magnetic resonance (NMR) spectra of the molecules they bind to. These effects...

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Bibliographic Details
Published in:Magnetic Resonance : (Göttingen) 2020-02, Vol.1 (1), p.1-12
Main Authors: Orton, Henry William, Huber, Thomas, Otting, Gottfried
Format: Article
Language:English
Subjects:
Algorithms
Anisotropy
Binding sites
Chemical equilibrium
Computer programs
Couplings
Datasets
Graphical user interface
Magnetic fields
Magnetic permeability
Magnetic susceptibility
Mathematical analysis
Metal ions
Molecular structure
NMR
Nuclear magnetic resonance
Open source software
Software
Source code
Tensors
User interface
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Summary:Paramagnetic metal ions with fast-relaxing electrons generate pseudocontact shifts (PCSs), residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) and cross-correlated relaxation (CCR) in the nuclear magnetic resonance (NMR) spectra of the molecules they bind to. These effects offer long-range structural information in molecules equipped with binding sites for such metal ions. Here we present the new open-source software Paramagpy, which has been written in Python 3 with a graphic user interface. Paramagpy combines the functionalities of different currently available programs to support the fitting of magnetic susceptibility tensors using PCS, RDC, PRE and CCR data and molecular coordinates in Protein Data Bank (PDB) format, including a convenient graphical user interface. Paramagpy uses efficient fitting algorithms to avoid local minima and supports corrections to back-calculated PCS and PRE data arising from cross-correlation effects with chemical shift tensors. The source code is available from 10.5281/zenodo.3594568 .
ISSN:2699-0016
2699-0016
DOI:10.5194/mr-1-1-2020