.. -*- coding: utf-8 -*-
.. _references:

************
 References
************


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`_


.. _references-components:

Citations for included algorithms and modules
=============================================

If you use the RMSD calculation (:mod:`MDAnalysis.analysis.rms`) or
alignment code (:mod:`MDAnalysis.analysis.align`) that uses the
:mod:`~MDAnalysis.core.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
:mod:`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
:mod:`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
:mod:`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
:mod:`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!

.. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787
.. _HELANAL: http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html
.. _`10.1371/journal.pcbi.1004568`: http://dx.doi.org/10.1371/journal.pcbi.1004568
