9. References

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 102 – 109, Austin, TX, 2016. SciPy. doi:10.25080/majora-629e541a-00e.

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 PMCID:PMC3144279

Beckstein2009

O Beckstein. EJ Denning, JR Perilla, and TB Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open/Closed Transitions. J Mol Biol 394 (2009), 160–176. doi:10.1016/j.jmb.2009.09.009

Seyler2014

L. Seyler and O. Beckstein. Sampling of large conformational transitions: Adenylate kinase as a testing ground. Molec. Simul. 40 (2014), 855–877. doi: 10.1080/08927022.2014.919497.