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The structures were visualized and hydrogen bonds were identified using PyMOL 1.3 (DeLano Scientific LLC, South San Francisco, CA, USA).
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Hydrogen bonding interactions between ligands and binding site residues were identified using the hydrogen bond monitor function in ViewerLite (www.accelrys.com).
Although the sampling is by no means comprehensive, five different states were identified using hydrogen bonding and base stacking as reaction coordinates.
Potential hydrogen bonds in the FimH-oligomannose-3 complex were identified using HBPLUS [70].
Hydrogen bond partner(s) to the conserved, buried polar residues were identified using the program, HBOND (J. Overington, unpublished).
Pharmacophore sites were identified using both point and vector geometries for the following features: H-bond donor, H-bond acceptor, ring, ionic, and hydrophobe.
26 bodies were identified using DNA tests.
The first-degree protein- and DNA-interaction partners of the 15 CoTs were identified using BOND™ in order to construct the signaling networks in which they operate.
Lipids were identified using internal spectral library.
All elephants were identified using distinctive markings.
Pathways were identified using global test [38].
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