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.

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!

[ALB93]

Andrea Amadei, Antonius B. M. Linssen, and Herman J. C. Berendsen. Essential dynamics of proteins. Proteins: Structure, Function, and Bioinformatics, 17(4):412–425, 1993. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.340170408. URL: http://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170408 (visited on 2021-01-05), doi:https://doi.org/10.1002/prot.340170408.

[BKV00]

M. Bansal, S. Kumar, and R. Velavan. HELANAL: a program to characterize helix geometry in proteins. Journal of Biomolecular Structure & Dynamics, 17(5):811–819, April 2000. 00175. doi:10.1080/07391102.2000.10506570.

[BDPW09]

Oliver Beckstein, Elizabeth J. Denning, Juan R. Perilla, and Thomas B. Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open↔Closed Transitions. Journal of Molecular Biology, 394(1):160–176, November 2009. 00107. URL: https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164 (visited on 2020-02-05), doi:10.1016/j.jmb.2009.09.009.

[BHE13]

R. B. Best, G. Hummer, and W. A. Eaton. Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences, 110(44):17874–17879, October 2013. 00259. URL: http://www.pnas.org/cgi/doi/10.1073/pnas.1311599110 (visited on 2020-02-05), doi:10.1073/pnas.1311599110.

[CL06]

Ronald R. Coifman and Stéphane Lafon. Diffusion maps. Applied and Computational Harmonic Analysis, 21(1):5–30, July 2006. 02271. doi:10.1016/j.acha.2006.04.006.

[dlPHHvdW08]

J. de la Porte, B. M. Herbst, W. Hereman, and S. J. van der Walt. An introduction to diffusion maps. In In The 19th Symposium of the Pattern Recognition Association of South Africa. 2008. 00038.

[FPKD11]

Andrew Ferguson, Athanassios Z. Panagiotopoulos, Ioannis G. Kevrekidis, and Pablo G. Debenedetti. Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach. Chemical Physics Letters, 509(1-3):1–11, June 2011. 00085. doi:10.1016/j.cplett.2011.04.066.

[FKDD07]

Joel Franklin, Patrice Koehl, Sebastian Doniach, and Marc Delarue. MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Research, 35(suppl_2):W477–W482, July 2007. 00083. URL: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkm342 (visited on 2020-02-05), doi:10.1093/nar/gkm342.

[GLB+16]

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.

[HKP+07]

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, September 2007. 00020. URL: https://doi.org/10.1021/ja071797y (visited on 2020-02-05), doi:10.1021/ja071797y.

[Hes02]

Berk Hess. Convergence of sampling in protein simulations. Physical Review E, 65(3):031910, March 2002. 00348. URL: https://link.aps.org/doi/10.1103/PhysRevE.65.031910 (visited on 2020-03-07), doi:10.1103/PhysRevE.65.031910.

[JWLM78]

Joël Janin, Shoshanna Wodak, Michael Levitt, and Bernard Maigret. Conformation of amino acid side-chains in proteins. Journal of Molecular Biology, 125(3):357 – 386, 1978. 00874. URL: http://www.sciencedirect.com/science/article/pii/0022283678904084, doi:10.1016/0022-2836(78)90408-4.

[Jol02]

I. T. Jolliffe. Principal Component Analysis. Springer Series in Statistics. Springer-Verlag, New York, 2 edition, 2002. ISBN 978-0-387-95442-4. URL: http://www.springer.com/gp/book/9780387954424 (visited on 2021-01-05), doi:10.1007/b98835.

[LAT09]

Pu Liu, Dimitris K. Agrafiotis, and Douglas L. Theobald. Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, pages n/a–n/a, 2009. URL: http://doi.wiley.com/10.1002/jcc.21439 (visited on 2020-02-05), doi:10.1002/jcc.21439.

[LDA+03]

Simon C. Lovell, Ian W. Davis, W. Bryan Arendall, Paul I. W. de Bakker, J. Michael Word, Michael G. Prisant, Jane S. Richardson, and David C. Richardson. Structure validation by Cα geometry: ϕ,ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics, 50(3):437–450, January 2003. 03997. URL: http://doi.wiley.com/10.1002/prot.10286 (visited on 2020-02-06), doi:10.1002/prot.10286.

[MLS09]

Gia G. Maisuradze, Adam Liwo, and Harold A. Scheraga. Principal component analysis for protein folding dynamics. Journal of molecular biology, 385(1):312–329, January 2009. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652707/ (visited on 2020-12-27), doi:10.1016/j.jmb.2008.10.018.

[MADWB11]

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, July 2011. 00778. URL: http://doi.wiley.com/10.1002/jcc.21787 (visited on 2020-02-05), doi:10.1002/jcc.21787.

[NCR18]

Hai Nguyen, David A Case, and Alexander S Rose. NGLview–interactive molecular graphics for Jupyter notebooks. Bioinformatics, 34(7):1241–1242, April 2018. 00024. URL: https://academic.oup.com/bioinformatics/article/34/7/1241/4721781 (visited on 2020-02-05), doi:10.1093/bioinformatics/btx789.

[RZMC11]

Mary A. Rohrdanz, Wenwei Zheng, Mauro Maggioni, and Cecilia Clementi. Determination of reaction coordinates via locally scaled diffusion map. The Journal of Chemical Physics, 134(12):124116, March 2011. 00220. doi:10.1063/1.3569857.

[SB17]

Sean Seyler and Oliver Beckstein. Molecular dynamics trajectory for benchmarking MDAnalysis. June 2017. 00002. URL: https://figshare.com/articles/Molecular_dynamics_trajectory_for_benchmarking_MDAnalysis/5108170 (visited on 2020-02-09), doi:10.6084/m9.figshare.5108170.v1.

[SKTB15]

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):e1004568, October 2015. URL: https://dx.plos.org/10.1371/journal.pcbi.1004568 (visited on 2020-02-05), doi:10.1371/journal.pcbi.1004568.

[SFPG+19]

Max Linke Shujie Fan, Ioannis Paraskevakos, Richard J. Gowers, Michael Gecht, and Oliver Beckstein. PMDA - Parallel Molecular Dynamics Analysis. In Chris Calloway, David Lippa, Dillon Niederhut, and David Shupe, editors, Proceedings of the 18th Python in Science Conference, 134 – 142. 2019. doi:10.25080/Majora-7ddc1dd1-013.

[SJS14]

Florian Sittel, Abhinav Jain, and Gerhard Stock. Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates. The Journal of Chemical Physics, 141(1):014111, July 2014. doi:10.1063/1.4885338.

[SS18]

Florian Sittel and Gerhard Stock. Perspective: Identification of collective variables and metastable states of protein dynamics. The Journal of Chemical Physics, 149(15):150901, October 2018. Publisher: American Institute of Physics. URL: http://aip.scitation.org/doi/10.1063/1.5049637 (visited on 2021-01-05), doi:10.1063/1.5049637.

[SGW93]

O S Smart, J M Goodfellow, and B A Wallace. The pore dimensions of gramicidin A. Biophysical Journal, 65(6):2455–2460, December 1993. 00522. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1225986/ (visited on 2020-02-10), doi:10.1016/S0006-3495(93)81293-1.

[SNW+96]

O. S. Smart, J. G. Neduvelil, X. Wang, B. A. Wallace, and M. S. Sansom. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Journal of Molecular Graphics, 14(6):354–360, 376, December 1996. 00935. doi:10.1016/s0263-7855(97)00009-x.

[SFSB14]

Lukas S. Stelzl, Philip W. Fowler, Mark S. P. Sansom, and Oliver Beckstein. Flexible gates generate occluded intermediates in the transport cycle of LacY. Journal of Molecular Biology, 426(3):735–751, February 2014. 00000. URL: https://asu.pure.elsevier.com/en/publications/flexible-gates-generate-occluded-intermediates-in-the-transport-c (visited on 2020-02-10), doi:10.1016/j.jmb.2013.10.024.

[SM67]

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. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/bip.1967.360050708, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/bip.1967.360050708, doi:https://doi.org/10.1002/bip.1967.360050708.

[The05]

Douglas L. Theobald. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4):478–480, July 2005. 00127. URL: http://scripts.iucr.org/cgi-bin/paper?S0108767305015266 (visited on 2020-02-05), doi:10.1107/S0108767305015266.

[TPB+15]

Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen. ENCORE: Software for Quantitative Ensemble Comparison. PLOS Computational Biology, 11(10):e1004415, October 2015. 00031. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004415 (visited on 2020-02-05), doi:10.1371/journal.pcbi.1004415.

[Wel62]

B. P. Welford. Note on a Method for Calculating Corrected Sums of Squares and Products. Technometrics, 4(3):419–420, August 1962. URL: https://amstat.tandfonline.com/doi/abs/10.1080/00401706.1962.10490022 (visited on 2020-02-10), doi:10.1080/00401706.1962.10490022.