13. References¶
13.1. Citation for the whole MDAnalysis library¶
When using MDAnalysis in published work, please cite
- 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
13.2. 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
- 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
- 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
- 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-Secchi, R., 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 (2014). Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Biophysical Journal, 107 (3), 599-612.
If you use the Path Similarity Analysis (PSA) code in
MDAnalysis.analysis.psa
please cite
- Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput Biol 11(10): e1004568. doi: 10.1371/journal.pcbi.1004568
Thanks!