@article {2022|2158,
	title = {Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions},
	journal = {Proteins: Structure, Function, and Bioinformatics},
	volume = {90},
	year = {2022},
	pages = {858-868},
	abstract = {<p>Abstract Tripeptide loop closure (TLC) is a standard procedure to reconstruct protein backbone conformations, by solving a zero-dimensional polynomial system yielding up to 16 solutions. In this work, we first show that multiprecision is required in a TLC solver to guarantee the existence and the accuracy of solutions. We then compare solutions yielded by the TLC solver against tripeptides from the Protein Data Bank. We show that these solutions are geometrically diverse (up to Root mean square deviation with respect to the data) and sound in terms of potential energy. Finally, we compare Ramachandran distributions of data and reconstructions for the three amino acids. The distribution of reconstructions in the second angular space stands out, with a rather uniform distribution leaving a central void. We anticipate that these insights, coupled to our robust implementation in the Structural Bioinformatics Library ( https://sbl.inria.fr/doc/Tripeptide_loop_closure-user-manual.html), will help understanding the properties of TLC reconstructions, with potential applications to the generation of conformations of flexible loops in particular.</p>
},
	keywords = {protein loop conformations, Ramachandran diagrams, robust numerics, tripeptide loop closure, tripeptides},
	doi = {https://doi.org/10.1002/prot.26281},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.26281},
	author = {O{\textquoteright}Donnell, Timoth{\'e}e and Robert, Charles H. and Cazals, Fr{\'e}d{\'e}ric}
}
@article {2013|1814,
	title = {Towards Morse theory for point cloud data.},
	journal = {Inria Tech Reports},
	number = {8331},
	year = {2013},
	publisher = {Inria},
	url = {http://hal.inria.fr/hal-00848753},
	author = {F. Cazals and C. Mueller and C. Robert and A. Roth}
}
@article {1994|1968,
	title = {Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy},
	journal = {Proc. Natl. Acad. Sci. U.s.a.},
	volume = {91},
	number = {24},
	year = {1994},
	month = {nov},
	pages = {11621{\textendash}11625},
	abstract = {Unfixed chicken erythrocyte chromatin fibers in very low salt have been imaged with a scanning force microscope operating in the tapping mode in air at ambient humidity. These images reveal a three-dimensional organization of the fibers. The planar "zig-zag" conformation is rare, and extended "beads-on-a-string" fibers are seen only in chromatin depleted of histones H1 and H5. Glutaraldehyde fixation reveals very similar structures. Fibers fixed in 10 mM salt appear somewhat more compacted. These results, when compared with modeling studies, suggest that chromatin fibers may exist as irregular three-dimensional arrays of nucleosomes even at low ionic strength.},
	keywords = {Animals, Atomic Force, Biological, Chickens, Chromatin, Fixatives, Histones, Microscopy, Models, Non-P.H.S., Non-U.S. Gov{\textquoteright}t, Osmolar Concentration, P.H.S., Research Support, Sodium Chloride, U.S. Gov{\textquoteright}t},
	author = {S. H. Leuba and G. Yang and C. Robert and B. Samori and K. van Holde and J. Zlatanova and C. Bustamante}
}
