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‎doc/source/examples/analysis/trajectory_similarity/harmonic_ensemble_similarity.ipynb‎

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"shell.execute_reply": "2021-05-19T06:03:04.424122Z"
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"/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/coordinates/memory.py:535: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911\n",
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"\n",
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"[4] Beckstein O, Denning EJ, Perilla JR, Woolf TB. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. *J Mol Biol*. 2009;394(1):160–176. [doi:10.1016/j.jmb.2009.09.009](https://dx.doi.org/10.1016%2Fj.jmb.2009.09.009)\n"
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"## References\n",
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"\n",
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"[1] Oliver Beckstein, Elizabeth&nbsp;J. Denning, Juan&nbsp;R. Perilla, and Thomas&nbsp;B. Woolf.\n",
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"Zipping and <span class=\"bibtex-protected\">Unzipping</span> of <span class=\"bibtex-protected\">Adenylate</span> <span class=\"bibtex-protected\">Kinase</span>: <span class=\"bibtex-protected\">Atomistic</span> <span class=\"bibtex-protected\">Insights</span> into the <span class=\"bibtex-protected\">Ensemble</span> of <span class=\"bibtex-protected\">Open</span>↔<span class=\"bibtex-protected\">Closed</span> <span class=\"bibtex-protected\">Transitions</span>.\n",
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"<em>Journal of Molecular Biology</em>, 394(1):160–176, November 2009.\n",
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"00107.\n",
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"URL: <a href=\"https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164\">https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164</a>, <a href=\"https://doi.org/10.1016/j.jmb.2009.09.009\">doi:10.1016/j.jmb.2009.09.009</a>.\n",
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"\n",
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"[2] Richard&nbsp;J. Gowers, Max Linke, Jonathan Barnoud, Tyler J.&nbsp;E. Reddy, Manuel&nbsp;N. Melo, Sean&nbsp;L. Seyler, Jan Domański, David&nbsp;L. Dotson, Sébastien Buchoux, Ian&nbsp;M. Kenney, and Oliver Beckstein.\n",
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"<span class=\"bibtex-protected\">MDAnalysis</span>: <span class=\"bibtex-protected\">A</span> <span class=\"bibtex-protected\">Python</span> <span class=\"bibtex-protected\">Package</span> for the <span class=\"bibtex-protected\">Rapid</span> <span class=\"bibtex-protected\">Analysis</span> of <span class=\"bibtex-protected\">Molecular</span> <span class=\"bibtex-protected\">Dynamics</span> <span class=\"bibtex-protected\">Simulations</span>.\n",
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"<em>Proceedings of the 15th Python in Science Conference</em>, pages 98–105, 2016.\n",
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"00152.\n",
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"URL: <a href=\"https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html\">https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html</a>, <a href=\"https://doi.org/10.25080/Majora-629e541a-00e\">doi:10.25080/Majora-629e541a-00e</a>.\n",
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"\n",
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"[3] Naveen Michaud-Agrawal, Elizabeth&nbsp;J. Denning, Thomas&nbsp;B. Woolf, and Oliver Beckstein.\n",
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"<span class=\"bibtex-protected\">MDAnalysis</span>: <span class=\"bibtex-protected\">A</span> toolkit for the analysis of molecular dynamics simulations.\n",
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"<em>Journal of Computational Chemistry</em>, 32(10):2319–2327, July 2011.\n",
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"00778.\n",
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"URL: <a href=\"http://doi.wiley.com/10.1002/jcc.21787\">http://doi.wiley.com/10.1002/jcc.21787</a>, <a href=\"https://doi.org/10.1002/jcc.21787\">doi:10.1002/jcc.21787</a>.\n",
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"\n",
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"[4] Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen.\n",
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"<span class=\"bibtex-protected\">ENCORE</span>: <span class=\"bibtex-protected\">Software</span> for <span class=\"bibtex-protected\">Quantitative</span> <span class=\"bibtex-protected\">Ensemble</span> <span class=\"bibtex-protected\">Comparison</span>.\n",
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"<em>PLOS Computational Biology</em>, 11(10):e1004415, October 2015.\n",
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"00031.\n",
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"URL: <a href=\"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004415\">https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004415</a>, <a href=\"https://doi.org/10.1371/journal.pcbi.1004415\">doi:10.1371/journal.pcbi.1004415</a>."
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‎doc/source/examples/constructing_universe.ipynb‎

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"Using MDAnalysis version 2.6.0-dev0\n"
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