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	url = {https://www.sciencedirect.com/science/article/pii/B9780080507545500694},
	author = {Spencer W. Thomas},
    id = {transformations}
}

@incollection{Goldman1991-transformation,
	title = {VII.2 - RECOVERING THE DATA FROM THE TRANSFORMATION MATRIX},
	editor = {James Arvo},
	booktitle = {Graphics Gems II},
	publisher = {Morgan Kaufmann},
	address = {San Diego},
	pages = {324-331},
	year = {1991},
	isbn = {978-0-08-050754-5},
	doi = {https://doi.org/10.1016/B978-0-08-050754-5.50070-0},
	url = {https://www.sciencedirect.com/science/article/pii/B9780080507545500700},
	author = {Ronald N. Goldman},
    id = {transformations}
}

@incollection{Shoemake1994-Euler,
	author = {Ken Shoemake},
	title = {Euler Angle Conversion},
	booktitle = {Graphics Gems IV},
	editor = {Paul S. Heckbert},
	publisher = {Morgan Kaufmann},
	year = {1994},
	pages = {222--229},
    id = {transformations}
}

@incollection{Shoemake1991-Arcball,
	author = {Ken Shoemake},
	title = {Arcball Rotation Control},
	booktitle = {Graphics Gems IV},
	editor = {Paul S. Heckbert},
	publisher = {Morgan Kaufmann},
	year = {1994},
	pages = {175--192},
    id = {transformations}
}

@incollection{Shoemake1991-Quaternions,
	author = {Ken Shoemake},
	title = {Quaternions},
    booktitle = {},
    year = {},
    url = {https://www.ljll.math.upmc.fr/~frey/papers/scientific%20visualisation/Shoemake%20K.,%20Quaternions.pdf},
    id = {transformations}
}

@incollection{Diebel2006,
	author = {Diebel, James},
	year = {2006},
	title = {Representing Attitude: Euler Angles, Unit Quaternions, and Rotation Vectors},
    booktitle = {},
    id = {transformations}
}

@article{Kabsch1978,
	author = "Kabsch, W.",
	title = "{A discussion of the solution for the best rotation to relate two sets of vectors}",
	journal = "Acta Crystallographica Section A",
	year = "1978",
	volume = "34",
	number = "5",
	pages = "827--828",
	month = "Sep",
	doi = {10.1107/S0567739478001680},
	url = {https://doi.org/10.1107/S0567739478001680},
    id = {transformations}
}

@article{Horn1987,
	author = {Horn, Berthold},
	year = {1987},
	month = {04},
	pages = {629-642},
	title = {Closed-Form Solution of Absolute Orientation Using Unit Quaternions},
	volume = {4},
	journal = {Journal of the Optical Society A},
	doi = {10.1364/JOSAA.4.000629},
    id = {transformations}
}

@incollection{Waveren2005
    title = {From Quaternion to Matrix and Back},
    author = {JMP van Waveren},
    year = {2005},
    url = {http://www.intel.com/cd/ids/developer/asmo-na/eng/293748.htm},
    booktitle = {},
    id = {transformations}
}

@article{Kulke2022,
  title = {Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations},
  author = {Kulke, Martin and Vermaas, Josh V.},
  year = {2022},
  journal = {Journal of Chemical Theory and Computation}, 
  volume = {18}, 
  number = {10},
  pages = {6161--6171},
  doi = {10.1021/acs.jctc.2c00327}
}

@article{Kabsch1983,
author = {Kabsch, Wolfgang and Sander, Christian},
title = {Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features},
journal = {Biopolymers},
volume = {22},
number = {12},
pages = {2577-2637},
doi = {https://doi.org/10.1002/bip.360221211},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bip.360221211},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/bip.360221211},
abstract = {Abstract For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.},
year = {1983}
}

@article{Linke2018,
  title = {Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations},
  author = {Linke, Max and Köfinger, Jürgen and Hummer, Gerhard},
  year = {2018},
  journal = {The Journal of Physical Chemistry B},
  volume = {122},
  number = {21},
  pages = {5630--5639},
  doi = {10.1021/acs.jpcb.7b11988}
}

@inproceedings{Fan2019,
  title = {{PMDA} - {P}arallel {M}olecular {D}ynamics {A}nalysis},
  author = {Shujie Fan and Max Linke and Ioannis Paraskevakos and Richard J. Gowers and Michael Gecht and Oliver Beckstein},
  year = {2019},
  booktitle = {{P}roceedings of the 18th {P}ython in {S}cience {C}onference},
  editor = {{C}hris {C}alloway and {D}avid {L}ippa and {D}illon {N}iederhut and {D}avid {S}hupe},
  organization = {SciPy},
  address = {Austin, TX},  
  pages = {134 - 142},
  doi = {10.25080/Majora-7ddc1dd1-013}
}
