A Practice Tutorial for Protein-Ligand Fingerprint Generation

1 A Practice Tutorial for Protein-Ligand Fingerprint Generation 

To use PLIF, it is necessary to assemble one or more proteins to serve as the receptor species and some ntrmber of li rtds with boimd conformations. Here, we will take example of a data set of Aitrora kinase A complexes having a bound ligand 

The computed fingerprints are written to the database field FP PLIF. Next, they are analysed (Fig. 9.47). 

The results are opened to show bar-code mode of fingerprints the display mode can also be changed to population mode where the residues are shown in their three letter codes and can be analysed to understand key interactions. This also shows residue corresponding to fingerprint bits (Fig. 9.48). 

Population display shows the fiequency of occurrence of residues. The show ligand option displays all the bound hgands in a 2D depict form. Here, it shows in nine out of ten complexes, the alanine residue is interacting with the aurora kinase protein (Fig. 9.49). 

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