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Figure 5 | BMC Bioinformatics

Figure 5

From: Towards accurate modeling of noncovalent interactions for protein rigidity analysis

Figure 5

Examples of generic and non-generic body-bar-hinge frameworks. Examples of generic and non-generic body-bar-hinge frameworks (a,b,c) and associated graphs (d,e,f). (a) shows a generic body-bar-hinge framework. The bar endpoints, and the continuous sets of points along the hinge axes, are all distinct. Its associated graph, shown in (d), is completely defined. The frameworks of (b,c) contain non-generic features described in this paper: a bar-bar concurrency (b) and a bar-hinge concurrency (c). These two types of degeneracies may occur in mechanical models of proteins when modeling H-bonds or hydrophobic interactions with a bar. Using our heuristic, we build associated graphs for the non-generic frameworks (e,f). Although for these two examples the pebble game will produce the correct result, there is no guarantee for non-generic cases.

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