Cargando…
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...
Autores principales: | , , |
---|---|
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 |
_version_ | 1785105967632875520 |
---|---|
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 . |
format | Online Article Text |
id | pubmed-10500712 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Copernicus GmbH |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT ortonhenrywilliam paramagpysoftwareforfittingmagneticsusceptibilitytensorsusingparamagneticeffectsmeasuredinnmrspectra AT huberthomas paramagpysoftwareforfittingmagneticsusceptibilitytensorsusingparamagneticeffectsmeasuredinnmrspectra AT ottinggottfried paramagpysoftwareforfittingmagneticsusceptibilitytensorsusingparamagneticeffectsmeasuredinnmrspectra |