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Figure 4 | BMC Bioinformatics

Figure 4

From: Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

Figure 4

Example of the tight superposition of similar ligands upon APF superposition of their binding sites: thiamine diphosphate in the binding sites of pyruvate dehydrogenase (1rp7, magenta) and pyruvate decarboxylase (1pvd, green). The resulting RMSD for thiamine ligand in this example is only 0.52A. At the same time even superimposable segments of the receptors’ secondary structure (transparent ribbons) experience much larger displacements. Sequence identity between the two proteins is 19.2%

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BMC Bioinformatics

ISSN: 1471-2105

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