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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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Detalles Bibliográficos
Autores principales: Orton, Henry William, Huber, Thomas, Otting, Gottfried
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Copernicus GmbH 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10500712/
https://www.ncbi.nlm.nih.gov/pubmed/37904891
http://dx.doi.org/10.5194/mr-1-1-2020
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author Orton, Henry William
Huber, Thomas
Otting, Gottfried
author_facet Orton, Henry William
Huber, Thomas
Otting, Gottfried
author_sort Orton, Henry William
collection PubMed
description 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 .
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spelling pubmed-105007122023-10-30 Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra Orton, Henry William Huber, Thomas Otting, Gottfried Magn Reson (Gott) Research Article 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 . Copernicus GmbH 2020-02-14 /pmc/articles/PMC10500712/ /pubmed/37904891 http://dx.doi.org/10.5194/mr-1-1-2020 Text en Copyright: © 2020 Henry William Orton et al. https://creativecommons.org/licenses/by/4.0/This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit https://creativecommons.org/licenses/by/4.0/
spellingShingle Research Article
Orton, Henry William
Huber, Thomas
Otting, Gottfried
Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra
title Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra
title_full Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra
title_fullStr Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra
title_full_unstemmed Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra
title_short Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra
title_sort paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in nmr spectra
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10500712/
https://www.ncbi.nlm.nih.gov/pubmed/37904891
http://dx.doi.org/10.5194/mr-1-1-2020
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