Fingerprint binding site

Fig. 5. Structural superposition of binding sites using Med-Sumo . The Surface Chemical Features (SCF) are used to superimpose the protein binding sites (toppanel).The SCF are represented in color code bar (bottom panel) and the SUMO score measure the quality of the 3D structural superimposition that is calculated using a bit-wise matching algorithm of the color code-bar fingerprint (bottom panel).

Fig. 10.1 The procedure used in the generation of the SIFt fingerprint, (a) 3D binding site of a kinase with a small molecule inhibitor bound, (b) sequence of the positions in the binding site in contact with the small molecule, together with their location in the structure of the kinase (g-loop and 3 to 4). Each binding site position is then represented by a bitstring, with each bit...

Figure 4.7. The complementaiy site points used for pharmacophore fingerprint calculations (lower right), together with the energetically favorable contours from 5 GRID probes on a FactorXa binding site.

Pharmacophore fingerprints derived from complementary site points to a target binding site have been used as a quantification of "biological diversity /structure-based diversity... 

Generate a protein fingerprint for each binding site. A protein fingerprint encodes the four point pharmacophore generated at step 3. 

Compare the protein fingerprints generated for different binding sites. This comparison, which does not require any alignment of the protein, produces similarity metrics. 

Fig. 2 Converting a reference protein-ligand complex (REF, bottom left) into an interaction fingerprint (IFP) registering seven possible interactions with binding site residues. Docked poses (bottom right) are fingerprinted and the corresponding IFPs compared to the reference IFP using a standard Tanimoto coefficient. The best pose (pose 6, bottom center) exhibits the highest IFP similarity to the reference...

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