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

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 98-105, Austin, TX, 2016. SciPy. 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 [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

If you use the hydrogen bond analysis code in MDAnalysis.analysis.hydrogenbonds.hbond_analysis please cite [Smith2019].

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] .

Amadei1999

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-Macias2004

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] .

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].

Calandri2011

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

Buyl2018

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].

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].

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].

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].

Buyl2013

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.

Jakupovic2021

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 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!