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Figure 15 | BMC Bioinformatics

Figure 15

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

Figure 15

Case study of Calmodulin (1ctr). In this case study, we demonstrate how varying the H-bonds and hydrophobic interactions included can produced a cluster decomposition that better matches with the 'gold standard'. (a-c) Rigid cluster decompositions of 1ctr by RigidFinder, KINARI v1.0 (method 3), and by varying hydrogen bonds and hydrophobic interactions (method 7). Using the RigidFinder decomposition as the gold standard for comparison, the decompositions of (b) and (c) attained, respectively, B-cubed scores of 0.48 and 0.90. (d) shows a plot of the B-cubed score as the energy cutoffs for H-bonds and hydrophobic interactions are varied, via method 7. To show how the H-bond and hydrophobic interaction energies are distributed, we include figures (e) and (f). The KINARI-Web server provides the functionality of viewing such histograms when choosing energy cutoffs.

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