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Figure 8 | BMC Research Notes

Figure 8

From: Searching the protein structure database for ligand-binding site similarities using CPASS v.2

Figure 8

Representative distribution curves showing the fraction of negatives and positives as a function of CPASS similarity scores for aspartate transaminases (PDB: 1yaa, EC 2.6.1.1). (A) A comparison of negatives (red) and positives (blue) CPASS similarity score distributions using a ligand-defined binding site (solid) and a manually-defined binding site (dashed). (B) A comparison of the fraction of negatives (red) and positives (blue) over the range of similarity scores for CPASS v.2, which includes the addition of Cβ in the RMSD calculation, ligand RMSD, and solvent accessible surface area (solid) to the original implementation of CPASS that lack these features (dashed). (C) A comparison of the fraction of negatives over the range of similarity scores for CPASS v.2 with all features (solid blue), CPASS v.2 without the addition of Cβ in the RMSD calculation (dashed red), CPASS v.2 without ligand RMSD and solvent accessible surface area (dotted purple), and CPASS v.1 (dash-dot green).

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