18. References
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.
18.1. Citations for the whole MDAnalysis library
When using MDAnalysis in published work, please cite [Michaud-Agrawal2011] and [Gowers2016].
(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
18.2. 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].
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.
If you use the helix analysis algorithm HELANAL in
MDAnalysis.analysis.helanal please cite [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].
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].
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].
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].
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].
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
If you use the hydrogen bond analysis code in
MDAnalysis.analysis.hydrogenbonds.hbond_analysis please cite [Smith2019].
P. Smith, R. M. Ziolek, E. Gazzarrini, D. M. Owen, and C. D. Lorenz. On the interaction of hyaluronic acid with synovial fluid lipid membranes. PCCP 21 (2019), 9845-9857. doi: 10.1039/C9CP01532A
If you use rmsip() or
rmsip() please cite [Amadei1999] and
[Leo-Macias2004] .
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
Leo-Macias, A., Lopez-Romero, P., Lupyan, D., Zerbino, D. & Ortiz, A. R. An Analysis of Core Deformations in Protein Superfamilies. Biophys J 88, 1291–1299 (2005). doi: 10.1529/biophysj.104.052449
If you use cumulative_overlap() or
cumulative_overlap() please cite [Yang2008] .
Yang, L., Song, G., Carriquiry, A. & Jernigan, R. L. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure 16, 321–330 (2008). doi: 10.1016/j.str.2007.12.011
If you use the Mean Squared Displacement analysis code in
MDAnalysis.analysis.msd please cite [Calandri2011] and [Buyl2018].
Calandrini, V., Pellegrini, E., Calligari, P., Hinsen, K., Kneller, G. R. NMoldyn-Interfacing Spectroscopic Experiments, Molecular Dynamics Simulations and Models for Time Correlation Functions. Collect. SFN, 12, 201–232 (2011). doi: 10.1051/sfn/201112010
Buyl, P. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), 877 (2018). doi: 10.21105/joss.00877
If you calculate shape parameters using
shape_parameter(),
shape_parameter(),
shape_parameter()
please cite [Dima2004a].
Dima, R. I., & Thirumalai, D. (2004). Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B, 108(21), 6564-6570. doi:10.1021/jp037128y
If you calculate asphericities using
asphericity(),
asphericity(),
asphericity()
please cite [Dima2004b].
Dima, R. I., & Thirumalai, D. (2004). Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B, 108(21), 6564-6570. doi:10.1021/jp037128y
If you use use the dielectric analysis code in
DielectricConstant please cite [Neumann1983].
Neumann, M. (1983). Dipole Moment Fluctuation Formulas in Computer Simulations of Polar Systems. Molecular Physics 50, no. 4, 841–858. doi: 10.1080/00268978300102721
If you use H5MD files using
MDAnalysis.coordinates.H5MD.py, please cite [Buyl2013] and
[Jakupovic2021].
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.
18.3. 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!