Jul 11, 2020

This package analyses molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments and spin-label to amide protein distances as probed in paramagnetic relaxation enhancement (PRE) experiments. The spin labels are fitted on trajectories and the spin label mobility is taken into account using a rotamer library.

When using this code please cite [Stelzl2014] and [Polyhach2011].

This package contains MTSL Rotamer libraries provided by Gunnar Jeschke (published under the GPL with his permission).

If you have questions or problems installing the package then ask on the MDAnalysis user mailing list:

Source code is available from under the open source GNU General Public License, version 2.



N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. J Comp Chem, 32:2319-2327, 2011. doi:10.1002/jcc.21787.


R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domański, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102 – 109, Austin, TX, 2016. SciPy.


Y. Polyhach, E. Bordignon, and G. Jeschke. Rotamer libraries of spin labelled cysteines for protein studies. Phys. Chem. Chem. Phys., 13:2356-2366, 2011. doi: 10.1039/C0CP01865A.


L. S. Stelz, P. W. Fowler, M. S. P. Sansom, and O. Beckstein. Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol, 426:735-751, 2013. doi: 10.1016/j.jmb.2013.10.024


P. W. Fowler, M. Orwick-Rydmark, S. Radestock, N. Solcan, P. M. Dijkman, J. A. Lyons, J. Kwok, M. Caffrey, A. Watts, L. R. Forrest, and S. Newstead. Gating topology of the proton-coupled oligopeptide symporters. Structure, 23:290–301, 2015. doi:10.1016/j.str.2014.12.012

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