@article{tiwari2007hbat,
  title={HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures},
  author={Tiwari, Abhishek and Panigrahi, Sunil Kumar},
  journal={In Silico Biology},
  volume={7},
  number={6},
  pages={651--661},
  year={2007},
  doi={10.3233/ISI-2007-00337},
  publisher={IOS Press}
}

@article{berman2000protein,
  title={The protein data bank},
  author={Berman, Helen M and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, T N and Weissig, Helge and Shindyalov, Ilya N and Bourne, Philip E},
  journal={Nucleic acids research},
  volume={28},
  number={1},
  pages={235--242},
  year={2000},
  publisher={Oxford University Press}
}

@article{mcdonald1994satisfying,
  title={Satisfying hydrogen bonding potential in proteins},
  author={McDonald, Iain K and Thornton, Janet M},
  journal={Journal of molecular biology},
  volume={238},
  number={5},
  pages={777--793},
  year={1994},
  publisher={Elsevier}
}

@article{lindauer1996hbexplore,
  title={HBexplore--a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules},
  author={Lindauer, Klaus and Bendic, Cvetko and S{\"u}hnel, J{\"u}rgen},
  journal={Computer applications in the biosciences: CABIOS},
  volume={12},
  number={4},
  pages={281--289},
  year={1996},
  publisher={Oxford University Press}
}

@article{harris2020numpy,
  title={Array programming with NumPy},
  author={Harris, Charles R and Millman, K Jarrod and Van Der Walt, St{\'e}fan J and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J and others},
  journal={Nature},
  volume={585},
  number={7825},
  pages={357--362},
  year={2020},
  publisher={Nature Publishing Group},
  doi={10.1038/s41586-020-2649-2}
}

@article{hunter2007matplotlib,
  title={Matplotlib: A 2D graphics environment},
  author={Hunter, John D},
  journal={Computing in science \& engineering},
  volume={9},
  number={3},
  pages={90--95},
  year={2007},
  publisher={IEEE Computer Society},
  doi={10.1109/MCSE.2007.55}
}

@inproceedings{hagberg2008networkx,
  title={Exploring network structure, dynamics, and function using NetworkX},
  author={Hagberg, Aric and Swart, Pieter and Chult, Daniel S},
  booktitle={Proceedings of the 7th Python in Science Conference},
  volume={11},
  pages={11--15},
  year={2008},
  organization={Pasadena, CA USA}
}

@misc{graphviz2024,
  title={Graphviz - Graph Visualization Software},
  author={{Graphviz Contributors}},
  year={2024},
  howpublished={\url{https://graphviz.org/}},
  note={Accessed: 2024-08-03}
}

@manual{tkinter2024,
  title={tkinter --- Python interface to Tcl/Tk},
  author={{Python Software Foundation}},
  year={2024},
  organization={Python Software Foundation},
  howpublished={\url{https://docs.python.org/3/library/tkinter.html}},
  note={Python Standard Library Documentation}
}
@article{salentin_plip_2015,
	title = {{PLIP}: fully automated protein-ligand interaction profiler},
	volume = {43},
	issn = {0305-1048},
	doi = {10.1093/nar/gkv315},
	number = {W1},
	journal = {Nucleic Acids Research},
	author = {Salentin, Sebastian and Schreiber, Sven and Haupt, V. Joachim and Adasme, Melissa F. and Schroeder, Michael},
	month = jul,
	year = {2015},
	pages = {W443--W447}
}

@article{jubb_arpeggio_2017,
	title = {Arpeggio: {A} {Web} {Server} for {Calculating} and {Visualising} {Interatomic} {Interactions} in {Protein} {Structures}},
	volume = {429},
	issn = {0022-2836},
	doi = {10.1016/j.jmb.2016.12.004},
	number = {3},
	journal = {Journal of Molecular Biology},
	author = {Jubb, Harry C and Higueruelo, Alicia P and Ochoa-Montaño, Bernardo and Pitt, Will R and Ascher, David B and Blundell, Tom L},
	month = feb,
	year = {2017},
	pages = {365--371}
}

@article{durrant_hbonanza_2011,
	title = {{HBonanza}: {A} {Computer} {Algorithm} for {Molecular}-{Dynamics}-{Trajectory} {Hydrogen}-{Bond} {Analysis}},
	volume = {31},
	issn = {1093-3263},
	doi = {10.1016/j.jmgm.2011.07.008},
	journal = {Journal of molecular graphics \& modelling},
	author = {Durrant, Jacob D. and McCammon, J. Andrew},
	month = nov,
	year = {2011},
	pages = {5--9}
}

@article{wang_hbcalculator_2024,
	title = {{HBCalculator}: {A} {Tool} for {Hydrogen} {Bond} {Distribution} {Calculations} in {Molecular} {Dynamics} {Simulations}},
	volume = {64},
	issn = {1549-9596},
	doi = {10.1021/acs.jcim.4c00054},
	number = {6},
	journal = {Journal of Chemical Information and Modeling},
	author = {Wang, Yulei and Wang, Yuxiang},
	month = mar,
	year = {2024},
	pages = {1772--1777}
}

@article{siemers_interactive_2021,
	title = {Interactive {Interface} for {Graph}-{Based} {Analyses} of {Dynamic} {H}-{Bond} {Networks}: {Application} to {Spike} {Protein} {S}},
	volume = {61},
	issn = {1549-9596},
	doi = {10.1021/acs.jcim.1c00306},
	number = {6},
	journal = {Journal of Chemical Information and Modeling},
	author = {Siemers, Malte and Bondar, Ana-Nicoleta},
	month = jun,
	year = {2021},
	pages = {2998--3014}
}

@misc{noauthor_431_nodate,
	title = {4.3.1. {Hydrogen} {Bond} {Analysis} - {MDAnalysis}.analysis.hydrogenbonds.hbond\_analysis},
	url = {https://docs.mdanalysis.org/1.1.0/documentation_pages/analysis/hydrogenbonds.html}
}

@misc{noauthor_gmx_nodate,
	title = {gmx hbond - {GROMACS} 2025.2 documentation},
	url = {https://manual.gromacs.org/current/onlinehelp/gmx-hbond.html}
}

@misc{noauthor_hbond_2020,
	title = {hbond - {AMBER}},
	url = {https://amberhub.chpc.utah.edu/hbond/},
	month = may,
	year = {2020}
}

@misc{noauthor_vmd_nodate,
	title = {{VMD} {HBonds} {Plugin}, {Version} 1.2},
	url = {https://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/}
}

@misc{noauthor_tool_nodate,
	title = {Tool: {H}-{Bonds}},
	url = {https://www.cgl.ucsf.edu/chimerax/docs/user/tools/hbonds.html}
}

@article{ferruz_proteintools_2021,
	title = {{ProteinTools}: a toolkit to analyze protein structures},
	volume = {49},
	issn = {0305-1048, 1362-4962},
	doi = {10.1093/nar/gkab375},
	number = {W1},
	journal = {Nucleic Acids Research},
	author = {Ferruz, Noelia and Schmidt, Steffen and Höcker, Birte},
	month = jul,
	year = {2021},
	pages = {W559--W566}
}

@article{mcgaughey_pi-stacking_1998,
	title = {π-{Stacking} {Interactions}: {ALIVE} {AND} {WELL} {IN} {PROTEINS}},
	volume = {273},
	issn = {0021-9258},
	doi = {10.1074/jbc.273.25.15458},
	number = {25},
	journal = {Journal of Biological Chemistry},
	author = {McGaughey, Georgia B. and Gagné, Marc and Rappé, Anthony K.},
	month = jun,
	year = {1998},
	pages = {15458--15463}
}

@article{vernon_pi-pi_nodate,
	title = {Pi-{Pi} contacts are an overlooked protein feature relevant to phase separation},
	volume = {7},
	issn = {2050-084X},
	doi = {10.7554/eLife.31486},
	journal = {eLife},
	author = {Vernon, Robert McCoy and Chong, Paul Andrew and Tsang, Brian and Kim, Tae Hun and Bah, Alaji and Farber, Patrick and Lin, Hong and Forman-Kay, Julie Deborah},
	year = {2018},
	pages = {e31486}
}

@article{rahim_reciprocal_2017,
	title = {Reciprocal carbonyl-carbonyl interactions in small molecules and proteins},
	volume = {8},
	issn = {2041-1723},
	doi = {10.1038/s41467-017-00081-x},
	number = {1},
	journal = {Nature Communications},
	author = {Rahim, Abdur and Saha, Pinaki and Jha, Kunal Kumar and Sukumar, Nagamani and Sarma, Bani Kanta},
	month = jul,
	year = {2017},
	pages = {78}
}

@article{newberry_n_2017,
	title = {The n→π* {Interaction}},
	volume = {50},
	issn = {0001-4842},
	doi = {10.1021/acs.accounts.7b00121},
	number = {8},
	journal = {Accounts of Chemical Research},
	author = {Newberry, Robert W. and Raines, Ronald T.},
	month = aug,
	year = {2017},
	pages = {1838--1846}
}

@article{choudhary_nature_2009,
	title = {Nature of {Amide} {Carbonyl}-{Carbonyl} {Interactions} in {Proteins}},
	volume = {131},
	issn = {0002-7863, 1520-5126},
	doi = {10.1021/ja901188y},
	number = {21},
	journal = {Journal of the American Chemical Society},
	author = {Choudhary, Amit and Gandla, Deepa and Krow, Grant R. and Raines, Ronald T.},
	month = jun,
	year = {2009},
	pages = {7244--7246}
}

@book{desiraju_weak_2001,
	title = {The {Weak} {Hydrogen} {Bond}},
	isbn = {978-0-19-850970-7},
	publisher = {Oxford University Press},
	author = {Desiraju, Gautam and Steiner, Thomas},
	month = may,
	year = {2001},
	doi = {10.1093/acprof:oso/9780198509707.001.0001}
}

@article{cavallo_halogen_2016,
	title = {The {Halogen} {Bond}},
	volume = {116},
	issn = {0009-2665},
	doi = {10.1021/acs.chemrev.5b00484},
	number = {4},
	journal = {Chemical Reviews},
	author = {Cavallo, Gabriella and Metrangolo, Pierangelo and Milani, Roberto and Pilati, Tullio and Priimagi, Arri and Resnati, Giuseppe and Terraneo, Giancarlo},
	month = feb,
	year = {2016},
	pages = {2478--2601}
}

@article{brandl_c-h-interactions_2001,
	title = {C-h⋯π-interactions in proteins},
	volume = {307},
	issn = {0022-2836},
	doi = {10.1006/jmbi.2000.4473},
	number = {1},
	journal = {Journal of Molecular Biology},
	author = {Brandl, Maria and Weiss, Manfred S. and Jabs, Andreas and Sühnel, Jürgen and Hilgenfeld, Rolf},
	month = mar,
	year = {2001},
	pages = {357--377}
}
