MDAnalysis and the included algorithms are scientific software that are described in academic publications. Please cite these papers when you use MDAnalysis in published work.
It is possible to automatically generate a list of references for any program that uses MDAnalysis. This list (in common reference manager formats) contains the citations associated with the specific algorithms and libraries that were used in the program.
17.1. Citations for the whole MDAnalysis library
(We are currently asking you to cite both papers if at all possible because the 2016 paper describes many updates to the original 2011 paper and neither paper on its own provides a comprehensive description of the library. We will publish a complete self-contained paper with the upcoming 1.0 release of MDAnalysis, which will then supersede these two citations.)
N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319–2327. 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. Domanski, 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 98-105, Austin, TX, 2016. SciPy. doi:10.25080/Majora-629e541a-00e
17.2. Citations for included algorithms and modules
Douglas L. Theobald. Rapid calculation of RMSD using a quaternion-based characteristic polynomial. Acta Crystallographica A 61 (2005), 478-480.
Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast determination of the optimal rotational matrix for macromolecular superpositions. J. Comput. Chem. 31 (2010), 1561–1563.
Bansal M, Kumar S, Velavan R. HELANAL — A program to characterise helix geometry in proteins. J. Biomol. Struct. Dyn. 17 (2000), 811–819
Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and Philip C. Biggin. Characterization of Protein Conformational States by Normal-Mode Frequencies. JACS 129 (2007), 11394–11401.
R. Araya-Secchi., Tomas Perez-Acle, Seung-gu Kang, Tien Huynh, Alejandro Bernardin, Yerko Escalona, Jose-Antonio Garate, Agustin D. Martinez, Isaac E. Garcia, Juan C. Saez, Ruhong Zhou. Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Biophysical Journal, 107 (2014), 599-612.
If you use the implementation of the ENCORE ensemble analysis in
MDAnalysis.analysis.encore please cite [Tiberti2015b].
Amadei, A., Ceruso, M. A. & Nola, A. D. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins’ molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics 36, 419–424 (1999). doi: 10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U
If you calculate shape parameters using
please cite [Dima2004a].
If you calculate asphericities using
please cite [Dima2004b].
Buyl P., Colberg P., and Höfling F.(2013). H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185. doi:10.1016/j.cpc.2014.01.018.
Jakupovic E. and Beckstein O., MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package, in Proceedings of the 20th Python in Science Conference, (Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe, eds.), pp. 18 – 26, 2021. doi:10.25080/majora-1b6fd038-005.
17.3. Citations using Duecredit
Citations can be automatically generated using duecredit, depending on the
packages used. Duecredit is easy to install via
pip. Simply type:
pip install duecredit
duecredit will remain an optional dependency, i.e. any code using MDAnalysis will work correctly even without duecredit installed.
A list of citations for
yourscript.py can be obtained using simple
cd /path/to/yourmodule python -m duecredit yourscript.py
or set the environment variable
DUECREDIT_ENABLE=yes python yourscript.py
Once the citations have been extracted (to a hidden file in the current directory), you can use the duecredit program to export them to different formats. For example, one can display them in BibTeX format, using:
duecredit summary --format=bibtex
Please cite your use of MDAnalysis and the packages and algorithms that it uses. Thanks!