Protein-ligand interaction fingerprint

Topological Scoring by Protein-Ligand Interaction Fingerprint (IFP)... 

Brewerton, S.C. (2008) The use of protein-ligand interaction fingerprints in docking. Current Opinion in Drug Discovery Development, 11, 356-364. 

Nandigam RK, Kim S, Singh J, Chuaqui C (2009) Position specific interaction dependent scoring technique for virtual screening based on weighted protein-ligand interaction fingerprint profiles. J Chem Inf Mod 49(5) 1185-1192... 

Analyzing Protein-Ligand Interactions Using Pharmacophore Fingerprints... 

Tan, L., Lounkine, E., and Bajorath, J. 2008. Similarity searching using fingerprints of molecular fragments involved in protein-ligand interactions. /. Chem. Inf. Model 48 2308-2312. 

Tan, L., Vogt, M., and Bajorath, J. 2009. Three-dimensional protein-ligand interaction scaling of two-dimensional fingerprints. Chem. Biol. Drug Des. 74 449-456. 

Deng et al. [18] recently described an approach to representing and analyzing 3D protein-ligand binding interactions. The Structural Interaction Fingerprint (SIFt see also Chapter 10) method represents a ligand by the interactions it un-... 

Deng, Z., Chuaqui, C., Singh, J., Structural interaction fingerprint (SI Ft) A novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem. 2004, 47, 337-344. 

In this chapter, we describe a simple and robust approach for representing and analyzing three-dimensional protein-ligand complexes called SIFt (Structural Interaction Fingerprint) [6, 7]. We will show how this method can be applied to organizing and analyzing the structural information within the protein kinase family and also how this can be applied to virtual screening for inhibitors. 

We have developed a profile-based approach termed p-SIFt [7] that enables us to describe the conservation of interactions between a set of protein-ligand receptor complexes. The use of profiles provides a sensitive means to compare and contrast multiple inhibitors binding to a drug target. A structural interaction fingerprint profile (p-SIFt) represents the degree to which interactions are conserved across a set of ligand-receptor complexes. The p-SIFt, P(r), is derived from an array, denoted below as b, of SIFt patterns and its derivation from a set of SIFts is shown in Fig. 10.2. 

Because the interaction fingerprint represents the binding mode of a ligand to a target protein, similar fingerprints imply that the corresponding ligands make similar interactions with the protein. 

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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