.. -*- coding: utf-8 -*- .. note: make sure that no lines accidentaly start with a single character .. followed by a period: reST interprets it as an enumerated list and .. messes up the formatting .. The references are accessible globally; you can cite these papers anywhere .. in the docs. .. _references: ************ 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 :ref:`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 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`_ .. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787 .. _`10.25080/Majora-629e541a-00e`: https://doi.org/10.25080/Majora-629e541a-00e .. _`MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations`: http://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html .. _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 [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 :mod:`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 .. _HELANAL: http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html If you use the GNM trajectory analysis code in :mod:`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 :mod:`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 :mod:`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`_ .. _`10.1371/journal.pcbi.1004568`: http://doi.org/10.1371/journal.pcbi.1004568 If you use the implementation of the ENCORE ensemble analysis in :mod:`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`_ .. _`10.1371/journal.pcbi.1004415`: http://doi.org/10.1371/journal.pcbi.1004415 If you use the streamline visualization in :mod:`MDAnalysis.visualization.streamlines` and :mod:`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`_ .. _`10.1039/c3fd00145h`: https://doi.org/10.1039/c3fd00145h If you use the hydrogen bond analysis code in :mod:`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`_ .. _`10.1039/C9CP01532A`: http://dx.doi.org/10.1039/C9CP01532A If you use :meth:`~MDAnalysis.analysis.pca.PCA.rmsip` or :func:`~MDAnalysis.analysis.pca.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`_ .. _`10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U`: https://doi.org/10.1002/(SICI)1097-0134(19990901)36:4%3C419::AID-PROT5%3E3.0.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`_ .. _`10.1529/biophysj.104.052449`: https://dx.doi.org/10.1529%2Fbiophysj.104.052449 If you use :meth:`~MDAnalysis.analysis.pca.PCA.cumulative_overlap` or :func:`~MDAnalysis.analysis.pca.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`_ .. _`10.1016/j.str.2007.12.011`: https://dx.doi.org/10.1016/j.str.2007.12.011 .. _citations-using-duecredit: Citations using Duecredit ========================= Citations can be automatically generated using duecredit_, depending on the packages used. Duecredit is easy to install via ``pip``. Simply type: .. code-block:: bash 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. .. code-block:: bash cd /path/to/yourmodule python -m duecredit yourscript.py or set the environment variable :envvar:`DUECREDIT_ENABLE` .. code-block:: bash DUECREDIT-ENABLE=yes python yourscript.py Once the citations have been extracted (to a hidden file in the current directory), you can use the :program:`duecredit` program to export them to different formats. For example, one can display them in BibTeX format, using: .. code-block:: bash duecredit summary --format=bibtex **Please cite your use of MDAnalysis and the packages and algorithms that it uses. Thanks!** .. _duecredit: https://github.com/duecredit/duecredit