15.2. 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].
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 |
Thanks!