15. References¶
15.1. Citations for the whole MDAnalysis library¶
When using MDAnalysis in published work, please cite [Michaud-Agrawal2011] and [Gowers2016].
[Michaud-Agrawal2011] | 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 |
[Gowers2016] | 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 102 – 109, Austin, TX, 2016. SciPy. |
15.2. Citations for included algorithms and modules¶
If you use the RMSD calculation (MDAnalysis.analysis.rms
) or alignment
code (MDAnalysis.analysis.align
) that uses the
qcprot
module please also cite [Theobald2005b] and
[Liu2010b].
[Theobald2005b] | Douglas L. Theobald. Rapid calculation of RMSD using a quaternion-based characteristic polynomial. Acta Crystallographica A 61 (2005), 478-480. |
[Liu2010b] | 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. |
If you use the helix analysis algorithm HELANAL in
MDAnalysis.analysis.helanal
please cite [Bansal2000b].
[Bansal2000b] | Bansal M, Kumar S, Velavan R. HELANAL — A program to characterise helix geometry in proteins. J. Biomol. Struct. Dyn. 17 (2000), 811–819 |
If you use the GNM trajectory analysis code in
MDAnalysis.analysis.gnm
please cite [Hall2007b].
[Hall2007b] | 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. |
If you use the water analysis code in
MDAnalysis.analysis.waterdynamics
please cite [Araya-Secchi2014b].
[Araya-Secchi2014b] | 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 Path Similarity Analysis (PSA) code in
MDAnalysis.analysis.psa
please cite [Seyler2015b].
[Seyler2015b] | Seyler SL, Kumar A, Thorpe MF, Beckstein O. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput Biol 11 (2015), e1004568. doi: 10.1371/journal.pcbi.1004568 |
If you use the implementation of the ENCORE ensemble analysis in
MDAnalysis.analysis.encore
please cite [Tiberti2015b].
[Tiberti2015b] | M. Tiberti, E. Papaleo, T. Bengtsen, W. Boomsma, and K. Lindorff-Larsen. ENCORE: Software for quantitative ensemble comparison. PLoS Comput Biol, 11 (2015), e1004415. doi: 10.1371/journal.pcbi.1004415 |
If you use the streamline visualization in
MDAnalysis.visualization.streamlines
and
MDAnalysis.visualization.streamlines_3D
please cite [Chavent2014b].
[Chavent2014b] | Chavent, M., Reddy, T., Dahl, C.E., Goose, J., Jobard, B., and Sansom, M.S.P. Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems. Faraday Discussions 169 (2014), 455–475. doi: 10.1039/c3fd00145h |
15.3. 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
commands.
cd /path/to/yourmodule
python -m duecredit yourscript.py
or set the environment variable DUECREDIT_ENABLE
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!