17. 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.
17.1. 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.)
- Michaud-Agrawal2011
Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf, and Oliver Beckstein. Mdanalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10):2319–2327, 2011. doi:10.1002/jcc.21787.
- Gowers2016
Richard J. Gowers, Max Linke, Jonathan Barnoud, Tyler J. E. Reddy, Manuel N. Melo, Sean L. Seyler, Jan Domański, David L. Dotson, Sébastien Buchoux, Ian M. Kenney, and Oliver Beckstein. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. Proceedings of the 15th Python in Science Conference, pages 98–105, 2016. 00152. URL: https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html (visited on 2020-02-05), doi:10.25080/Majora-629e541a-00e.
17.2. 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 [ᵃTheobald2005]
and [ᵃLiu2010].
- ᵃTheobald2005
Douglas L. Theobald. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A, 61(4):478–480, Jul 2005. doi:10.1107/S0108767305015266.
- ᵃLiu2010
Pu Liu, Dimitris K. Agrafiotis, and Douglas L. Theobald. Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7):1561–1563, 2010. doi:10.1002/jcc.21439.
If you use the HELANAL algorithm in
MDAnalysis.analysis.helix_analysis please cite [ᵃBansal2000, ᵃSugeta1967].
- ᵃBansal2000
Manju Bansal, Sandeep Kumart, and R. Velavan. Helanal: a program to characterize helix geometry in proteins. Journal of Biomolecular Structure and Dynamics, 17(5):811–819, 2000. PMID: 10798526. doi:10.1080/07391102.2000.10506570.
- ᵃSugeta1967
Hiromu Sugeta and Tatsuo Miyazawa. General method for calculating helical parameters of polymer chains from bond lengths, bond angles, and internal-rotation angles. Biopolymers, 5(7):673–679, 1967. doi:10.1002/bip.1967.360050708.
If you use the GNM trajectory analysis code in
MDAnalysis.analysis.gnm please cite [ᵃHall2007].
- ᵃHall2007
Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and Philip C. Biggin. Characterization of protein conformational states by normal-mode frequencies. Journal of the American Chemical Society, 129(37):11394–11401, 2007. PMID: 17715919. doi:10.1021/ja071797y.
If you use the water analysis code in
MDAnalysis.analysis.waterdynamics please cite [ᵃAraya-Secchi2014].
- ᵃAraya-Secchi2014
Raul Araya-Secchi, Tomas Perez-Acle, Seung-gu Kang, Tien Huynh, Alejandro Bernardin, Yerko Escalona, Jose-Antonio Garate, Agustin D. Martínez, Isaac E. García, Juan C. Sáez, and Ruhong Zhou. Characterization of a novel water pocket inside the human cx26 hemichannel structure. Biophysical Journal, 107(3):599–612, 2014. doi:10.1016/j.bpj.2014.05.037.
If you use the Path Similarity Analysis (PSA) code in
MDAnalysis.analysis.psa please [ᵃSeyler2015].
- ᵃSeyler2015
Sean L. Seyler, Avishek Kumar, M. F. Thorpe, and Oliver Beckstein. Path similarity analysis: a method for quantifying macromolecular pathways. PLOS Computational Biology, 11(10):1–37, 10 2015. doi:10.1371/journal.pcbi.1004568.
If you use the implementation of the ENCORE ensemble analysis in
MDAnalysis.analysis.encore please cite [ᵃTiberti2015].
- ᵃTiberti2015
Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen. Encore: software for quantitative ensemble comparison. PLOS Computational Biology, 11(10):1–16, 10 2015. doi:10.1371/journal.pcbi.1004415.
If you use the streamline visualization in
MDAnalysis.visualization.streamlines and
MDAnalysis.visualization.streamlines_3D please cite [ᵃChavent2014].
- ᵃChavent2014
Matthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl, John E. Stone, Bruno Jobard, and Mark S. P. Sansom. Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems. Faraday Discuss., 169:455–475, 2014. doi:10.1039/C3FD00145H.
If you use the hydrogen bond analysis code in
MDAnalysis.analysis.hydrogenbonds.hbond_analysis please cite [ᵃSmith2019].
- ᵃSmith2019
Paul Smith, Robert M. Ziolek, Elena Gazzarrini, Dylan M. Owen, and Christian D. Lorenz. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Phys. Chem. Chem. Phys., 21:9845–9857, 2019. doi:10.1039/C9CP01532A.
If you use rmsip() or
rmsip() please cite [ᵃAmadei1999] and
[ᵃLeo-Macias2005].
- ᵃAmadei1999
Andrea Amadei, Marc A. Ceruso, and Alfredo Di Nola. 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(4):419–424, 1999. doi:10.1080/07391102.2000.10506570.
- ᵃLeo-Macias2005
Alejandra Leo-Macias, Pedro Lopez-Romero, Dmitry Lupyan, Daniel Zerbino, and Angel R. Ortiz. An analysis of core deformations in protein superfamilies. Biophysical Journal, 88(2):1291–1299, 2005. doi:10.1529/biophysj.104.052449.
If you use cumulative_overlap() or
cumulative_overlap() please cite
[ᵃYang2008].
- ᵃYang2008
Lei Yang, Guang Song, Alicia Carriquiry, and Robert L. Jernigan. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2):321–330, February 2008. doi:10.1016/j.str.2007.12.011.
If you use the Mean Squared Displacement analysis code in
MDAnalysis.analysis.msd please cite [ᵃCalandrini2011] and
[ᵃBuyl2018].
- ᵃCalandrini2011
Vania Calandrini, Eric Pellegrini, Konrad Hinsen, and Gerald Kneller. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions, pages 201–232. Volume 12. 01 2011. doi:10.1051/sfn/201112010.
- ᵃBuyl2018
Pierre Buyl. Tidynamics: a tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3:877, 08 2018. doi:10.21105/joss.00877.
If you calculate shape parameters using
shape_parameter(),
shape_parameter(),
shape_parameter(),
or if you calculate asphericities using
asphericity(),
asphericity(),
asphericity(),
please cite [ᵃDima2004].
- ᵃDima2004
Ruxandra I. Dima and D. Thirumalai. Asymmetry in the shapes of folded and denatured states of proteins. The Journal of Physical Chemistry B, 108(21):6564–6570, 2004. doi:10.1021/jp037128y.
If you use use the dielectric analysis code in
DielectricConstant please cite
[ᵃNeumann1983].
- ᵃNeumann1983
Martin Neumann. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4):841–858, 1983. doi:10.1080/00268978300102721.
If you use H5MD files with
MDAnalysis.coordinates.H5MD, please cite [ᵃde Buyl2014] and
[ᵃJakupovic2021].
- ᵃde Buyl2014
Pierre de Buyl, Peter H. Colberg, and Felix Höfling. H5md: a structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6):1546–1553, 2014. doi:10.1016/j.cpc.2014.01.018.
- ᵃJakupovic2021
Edis Jakupovic and Oliver Beckstein. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe, editors, Proceedings of the 20th Python in Science Conference, 40–48. Austin, TX, 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
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!