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Figure 4 | BMC Bioinformatics

Figure 4

From: Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

Figure 4

Provar algorithm scores pocket-lining atoms and residues on each structure. Illustration of Provar applied to the same pocket on two simulated conformations of Abl kinase [PDB:2GQG]. For each structure, pocket atoms (top panels, yellow) are scored as pocket-lining if sites predicted to be pocket-lining (red spheres) are within a defined cut-off distance. Residues that contain pocket-lining atoms are also pocket-lining (mid panels, green). For each structure this generates one set of scores for each structure's atoms and another for its residues. The scores of individual structures can then be readily combined to calculate the proportion of the equivalent atoms or residues being pocket-lining within a set of structures.

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